https://launchpad.net/ubuntu/+archive/test-rebuild-20200327-focal/+build/18968999 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-011 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_189 python-lpbuildd_189 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 12 Apr 07:48:06 ntpdate[1915]: adjust time server 10.211.37.1 offset -0.001099 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-18968999 --image-type chroot /home/buildd/filecache-default/dd8fbbe4a386f61f7a7bfaa5a4cddb80aba54f91 Creating target for build PACKAGEBUILD-18968999 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-18968999 Starting target for build PACKAGEBUILD-18968999 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-18968999 'deb http://ftpmaster.internal/ubuntu focal main universe' Overriding sources.list in build-PACKAGEBUILD-18968999 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-18968999 Updating target for build PACKAGEBUILD-18968999 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [265 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main armhf Packages [936 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main Translation-en [503 kB] Get:4 http://ftpmaster.internal/ubuntu focal/universe armhf Packages [8322 kB] Get:5 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5131 kB] Fetched 15.2 MB in 6s (2712 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: systemd-timesyncd The following packages will be upgraded: apt binutils binutils-arm-linux-gnueabihf binutils-common bsdutils fdisk gcc-10-base libapparmor1 libapt-pkg6.0 libatomic1 libbinutils libblkid1 libcc1-0 libctf-nobfd0 libctf0 libfdisk1 libgcc-s1 libgomp1 libmount1 libsmartcols1 libstdc++6 libsystemd0 libubsan1 libudev1 libuuid1 login mount passwd pinentry-curses systemd systemd-sysv util-linux 32 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 12.2 MB of archives. After this operation, 164 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main armhf bsdutils armhf 1:2.34-0.1ubuntu9 [57.9 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main armhf login armhf 1:4.8.1-1ubuntu4 [218 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main armhf libblkid1 armhf 2.34-0.1ubuntu9 [124 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main armhf libuuid1 armhf 2.34-0.1ubuntu9 [19.4 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main armhf libfdisk1 armhf 2.34-0.1ubuntu9 [163 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main armhf libmount1 armhf 2.34-0.1ubuntu9 [135 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main armhf libsmartcols1 armhf 2.34-0.1ubuntu9 [88.5 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main armhf fdisk armhf 2.34-0.1ubuntu9 [109 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main armhf util-linux armhf 2.34-0.1ubuntu9 [957 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main armhf libatomic1 armhf 10-20200405-0ubuntu1 [7188 B] Get:11 http://ftpmaster.internal/ubuntu focal/main armhf libubsan1 armhf 10-20200405-0ubuntu1 [121 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main armhf libgomp1 armhf 10-20200405-0ubuntu1 [86.9 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main armhf gcc-10-base armhf 10-20200405-0ubuntu1 [18.5 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main armhf libgcc-s1 armhf 10-20200405-0ubuntu1 [36.2 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main armhf libcc1-0 armhf 10-20200405-0ubuntu1 [34.6 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main armhf libstdc++6 armhf 10-20200405-0ubuntu1 [440 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main armhf systemd-sysv armhf 245.4-2ubuntu1 [10.3 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main armhf systemd armhf 245.4-2ubuntu1 [3642 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main armhf systemd-timesyncd armhf 245.4-2ubuntu1 [27.9 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main armhf libapparmor1 armhf 2.13.3-7ubuntu4 [29.0 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main armhf mount armhf 2.34-0.1ubuntu9 [108 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main armhf libsystemd0 armhf 245.4-2ubuntu1 [249 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main armhf libudev1 armhf 245.4-2ubuntu1 [70.3 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main armhf libapt-pkg6.0 armhf 2.0.1ubuntu1 [752 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main armhf apt armhf 2.0.1ubuntu1 [1245 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main armhf passwd armhf 1:4.8.1-1ubuntu4 [750 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main armhf libctf0 armhf 2.34-6ubuntu1 [37.1 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main armhf binutils-arm-linux-gnueabihf armhf 2.34-6ubuntu1 [2093 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main armhf libbinutils armhf 2.34-6ubuntu1 [317 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main armhf binutils armhf 2.34-6ubuntu1 [3360 B] Get:31 http://ftpmaster.internal/ubuntu focal/main armhf binutils-common armhf 2.34-6ubuntu1 [207 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main armhf libctf-nobfd0 armhf 2.34-6ubuntu1 [37.9 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main armhf pinentry-curses armhf 1.1.0-3build1 [31.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.2 MB in 1s (22.7 MB/s) (Reading database ... 12561 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.34-0.1ubuntu9_armhf.deb ... Unpacking bsdutils (1:2.34-0.1ubuntu9) over (1:2.34-0.1ubuntu8) ... Setting up bsdutils (1:2.34-0.1ubuntu9) ... (Reading database ... 12561 files and directories currently installed.) Preparing to unpack .../login_1%3a4.8.1-1ubuntu4_armhf.deb ... Unpacking login (1:4.8.1-1ubuntu4) over (1:4.8.1-1ubuntu3) ... Setting up login (1:4.8.1-1ubuntu4) ... (Reading database ... 12561 files and directories currently installed.) Preparing to unpack .../libblkid1_2.34-0.1ubuntu9_armhf.deb ... Unpacking libblkid1:armhf (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Setting up libblkid1:armhf (2.34-0.1ubuntu9) ... (Reading database ... 12561 files and directories currently installed.) Preparing to unpack .../libuuid1_2.34-0.1ubuntu9_armhf.deb ... Unpacking libuuid1:armhf (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Setting up libuuid1:armhf (2.34-0.1ubuntu9) ... (Reading database ... 12561 files and directories currently installed.) Preparing to unpack .../libfdisk1_2.34-0.1ubuntu9_armhf.deb ... Unpacking libfdisk1:armhf (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Preparing to unpack .../libmount1_2.34-0.1ubuntu9_armhf.deb ... Unpacking libmount1:armhf (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Setting up libmount1:armhf (2.34-0.1ubuntu9) ... (Reading database ... 12561 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.34-0.1ubuntu9_armhf.deb ... Unpacking libsmartcols1:armhf (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Setting up libsmartcols1:armhf (2.34-0.1ubuntu9) ... (Reading database ... 12561 files and directories currently installed.) Preparing to unpack .../fdisk_2.34-0.1ubuntu9_armhf.deb ... Unpacking fdisk (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Preparing to unpack .../util-linux_2.34-0.1ubuntu9_armhf.deb ... Unpacking util-linux (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Setting up util-linux (2.34-0.1ubuntu9) ... (Reading database ... 12561 files and directories currently installed.) Preparing to unpack .../libatomic1_10-20200405-0ubuntu1_armhf.deb ... Unpacking libatomic1:armhf (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Preparing to unpack .../libubsan1_10-20200405-0ubuntu1_armhf.deb ... Unpacking libubsan1:armhf (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Preparing to unpack .../libgomp1_10-20200405-0ubuntu1_armhf.deb ... Unpacking libgomp1:armhf (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Preparing to unpack .../gcc-10-base_10-20200405-0ubuntu1_armhf.deb ... Unpacking gcc-10-base:armhf (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Setting up gcc-10-base:armhf (10-20200405-0ubuntu1) ... (Reading database ... 12561 files and directories currently installed.) Preparing to unpack .../libgcc-s1_10-20200405-0ubuntu1_armhf.deb ... Unpacking libgcc-s1:armhf (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Setting up libgcc-s1:armhf (10-20200405-0ubuntu1) ... (Reading database ... 12561 files and directories currently installed.) Preparing to unpack .../libcc1-0_10-20200405-0ubuntu1_armhf.deb ... Unpacking libcc1-0:armhf (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Preparing to unpack .../libstdc++6_10-20200405-0ubuntu1_armhf.deb ... Unpacking libstdc++6:armhf (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Setting up libstdc++6:armhf (10-20200405-0ubuntu1) ... (Reading database ... 12561 files and directories currently installed.) Preparing to unpack .../0-systemd-sysv_245.4-2ubuntu1_armhf.deb ... Unpacking systemd-sysv (245.4-2ubuntu1) over (245.2-1ubuntu2) ... Preparing to unpack .../1-systemd_245.4-2ubuntu1_armhf.deb ... Unpacking systemd (245.4-2ubuntu1) over (245.2-1ubuntu2) ... dpkg: warning: unable to delete old directory '/etc/dhcp/dhclient-exit-hooks.d': Directory not empty Selecting previously unselected package systemd-timesyncd. 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Unpacking libapt-pkg6.0:armhf (2.0.1ubuntu1) over (2.0.1) ... Setting up libapt-pkg6.0:armhf (2.0.1ubuntu1) ... (Reading database ... 12562 files and directories currently installed.) Preparing to unpack .../apt_2.0.1ubuntu1_armhf.deb ... Unpacking apt (2.0.1ubuntu1) over (2.0.1) ... Setting up apt (2.0.1ubuntu1) ... (Reading database ... 12562 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.8.1-1ubuntu4_armhf.deb ... Unpacking passwd (1:4.8.1-1ubuntu4) over (1:4.8.1-1ubuntu3) ... Setting up passwd (1:4.8.1-1ubuntu4) ... (Reading database ... 12562 files and directories currently installed.) Preparing to unpack .../0-libctf0_2.34-6ubuntu1_armhf.deb ... Unpacking libctf0:armhf (2.34-6ubuntu1) over (2.34-5ubuntu1) ... Preparing to unpack .../1-binutils-arm-linux-gnueabihf_2.34-6ubuntu1_armhf.deb ... Unpacking binutils-arm-linux-gnueabihf (2.34-6ubuntu1) over (2.34-5ubuntu1) ... Preparing to unpack .../2-libbinutils_2.34-6ubuntu1_armhf.deb ... 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Setting up libubsan1:armhf (10-20200405-0ubuntu1) ... Setting up mount (2.34-0.1ubuntu9) ... Setting up libbinutils:armhf (2.34-6ubuntu1) ... Setting up libcc1-0:armhf (10-20200405-0ubuntu1) ... Setting up libctf0:armhf (2.34-6ubuntu1) ... Setting up fdisk (2.34-0.1ubuntu9) ... Setting up binutils-arm-linux-gnueabihf (2.34-6ubuntu1) ... Setting up binutils (2.34-6ubuntu1) ... Setting up systemd (245.4-2ubuntu1) ... Created symlink /etc/systemd/system/systemd-remount-fs.service.wants/systemd-pstore.service -> /lib/systemd/system/systemd-pstore.service. Initializing machine ID from KVM UUID. Removing obsolete conffile /etc/dhcp/dhclient-exit-hooks.d/timesyncd ... Removing obsolete conffile /etc/systemd/timesyncd.conf ... Setting up systemd-timesyncd (245.4-2ubuntu1) ... Created symlink /etc/systemd/system/sysinit.target.wants/systemd-timesyncd.service -> /lib/systemd/system/systemd-timesyncd.service. Setting up systemd-sysv (245.4-2ubuntu1) ... Processing triggers for libc-bin (2.31-0ubuntu7) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18968999 armhf focal -c chroot:build-PACKAGEBUILD-18968999 --arch=armhf --dist=focal --nolog rdkit_201909.1-2ubuntu5.dsc Initiating build PACKAGEBUILD-18968999 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-011.buildd +==============================================================================+ | rdkit 201909.1-2ubuntu5 (armhf) 12 Apr 2020 07:48 | +==============================================================================+ Package: rdkit Version: 201909.1-2ubuntu5 Source Version: 201909.1-2ubuntu5 Distribution: focal Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/rdkit-6bdEUu/rdkit-201909.1' with '<>' I: NOTICE: Log filtering will replace 'build/rdkit-6bdEUu' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18968999/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- rdkit_201909.1-2ubuntu5.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-PmLOTZ/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-PmLOTZ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-PmLOTZ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-PmLOTZ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-PmLOTZ/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-PmLOTZ/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (68.4 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-PmLOTZ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (70.8 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12562 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: bison, cmake, debhelper (>> 9), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, libboost-iostreams-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libschroedinger-coordgenlibs-dev (>= 1.1-4), libschroedinger-maeparser-dev (>= 1.2-1), librsvg2-bin, libsqlite3-dev, pandoc, postgresql-server-dev-all, python3-dev, python3-numpy, python3-pandas, python3-pil | python3-imaging, python3-recommonmark, python3-sphinx, rapidjson-dev, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended Filtered Build-Depends: bison, cmake, debhelper (>> 9), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, libboost-iostreams-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libschroedinger-coordgenlibs-dev (>= 1.1-4), libschroedinger-maeparser-dev (>= 1.2-1), librsvg2-bin, libsqlite3-dev, pandoc, postgresql-server-dev-all, python3-dev, python3-numpy, python3-pandas, python3-pil | python3-imaging, python3-recommonmark, python3-sphinx, rapidjson-dev, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended dpkg-deb: building package 'sbuild-build-depends-rdkit-dummy' in '/<>/resolver-yaZWyb/apt_archive/sbuild-build-depends-rdkit-dummy.deb'. Ign:1 copy:/<>/resolver-yaZWyb/apt_archive ./ InRelease Get:2 copy:/<>/resolver-yaZWyb/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-yaZWyb/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-yaZWyb/apt_archive ./ Sources [437 B] Get:5 copy:/<>/resolver-yaZWyb/apt_archive ./ Packages [772 B] Fetched 3328 B in 0s (93.7 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install rdkit build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binfmt-support bison bsdmainutils clang-10 cmake cmake-data debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common doxygen dwz file flex fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern gettext gettext-base groff-base hicolor-icon-theme icu-devtools imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian latexmk libapache-pom-java libarchive-zip-perl libarchive13 libasn1-8-heimdal libblas3 libboost-atomic1.71-dev libboost-atomic1.71.0 libboost-chrono1.71-dev libboost-chrono1.71.0 libboost-date-time1.71-dev libboost-date-time1.71.0 libboost-dev libboost-iostreams-dev libboost-iostreams1.71-dev libboost-iostreams1.71.0 libboost-python-dev libboost-python1.71-dev libboost-python1.71.0 libboost-regex-dev libboost-regex1.71-dev libboost-regex1.71.0 libboost-serialization1.71-dev libboost-serialization1.71.0 libboost-system-dev libboost-system1.71-dev libboost-system1.71.0 libboost-thread-dev libboost-thread1.71-dev libboost-thread1.71.0 libboost1.71-dev libbrotli1 libbsd0 libcairo2 libclang-common-10-dev libclang-cpp10 libclang1-10 libcommons-logging-java libcommons-parent-java libcroco3 libcurl4 libdatrie1 libdebhelper-perl libedit2 libelf1 libexpat1 libexpat1-dev libffi-dev libfftw3-double3 libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfreetype6 libfribidi0 libgc1c2 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz-icu0 libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libice6 libicu-dev libicu66 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libjsoncpp1 libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libllvm10 liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-6 libmagickwand-6.q16-6 libmpdec2 libncurses-dev libnghttp2-14 libobjc-9-dev libobjc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpdfbox-java libpfm4 libpipeline1 libpixman-1-0 libpq-dev libpq5 libpsl5 libptexenc1 libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib librhash0 libroken18-heimdal librsvg2-2 librsvg2-bin librtmp1 libsasl2-2 libsasl2-modules-db libschroedinger-coordgenlibs-dev libschroedinger-coordgenlibs1 libschroedinger-maeparser-dev libschroedinger-maeparser1 libsigsegv2 libsm6 libsqlite3-dev libssh-4 libsub-override-perl libsynctex2 libteckit0 libtexlua53 libtexluajit2 libthai-data libthai0 libtiff5 libtinfo-dev libtool libuchardet0 libuv1 libwebp6 libwebpdemux2 libwebpmux3 libwind0-heimdal libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libyaml-0-2 libz3-4 libz3-dev libzzip-0-13 llvm-10 llvm-10-dev llvm-10-runtime llvm-10-tools m4 man-db mime-support netbase pandoc pandoc-data po-debconf postgresql-client-12 postgresql-client-common postgresql-common postgresql-server-dev-12 postgresql-server-dev-all preview-latex-style python-babel-localedata python3 python3-alabaster python3-babel python3-certifi python3-chardet python3-commonmark-bkrs python3-dateutil python3-dev python3-distutils python3-docutils python3-idna python3-imagesize python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pygments python3-pyparsing python3-recommonmark python3-requests python3-roman python3-six python3-sphinx python3-tz python3-urllib3 python3-yaml python3.8 python3.8-dev python3.8-minimal rapidjson-dev sgml-base shared-mime-info sphinx-common ssl-cert t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ucf x11-common xdg-utils xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bison-doc wamerican | wordlist whois vacation clang-10-doc cmake-doc ninja-build dh-make doxygen-latex doxygen-doc doxygen-gui graphviz flex-doc gettext-doc libasprintf-dev libgettextpo-dev groff imagemagick-doc autotrace cups-bsd | lpr | lprng curl enscript ffmpeg gimp gnuplot grads hp2xx html2ps libwmf-bin mplayer povray radiance sane-utils transfig ufraw-batch ghostscript lrzip libboost-doc libboost1.71-doc gccxml libboost-container1.71-dev libboost-context1.71-dev libboost-contract1.71-dev libboost-coroutine1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev libboost-filesystem1.71-dev libboost-graph1.71-dev libboost-graph-parallel1.71-dev libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev libboost-program-options1.71-dev libboost-random1.71-dev libboost-stacktrace1.71-dev libboost-test1.71-dev libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev libboost1.71-tools-dev libmpfrc++-dev libntl-dev libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java libfftw3-bin libfftw3-dev krb5-doc krb5-user icu-doc liblcms2-utils libmagickcore-6.q16-6-extra ncurses-doc postgresql-doc-12 sqlite3-doc libtool-doc gfortran | fortran95-compiler gcj-jdk xapian-tools llvm-10-doc m4-doc apparmor less www-browser texlive-xetex texlive-luatex pandoc-citeproc context wkhtmltopdf ghc nodejs php python ruby r-base-core libjs-mathjax node-katex libmail-box-perl postgresql-12 libjson-perl python3-doc python3-tk python3-venv python-commonmark-bkrs-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french python-jinja2-doc gfortran python-numpy-doc python3-pytest python3-numpy-dbg python-pandas-doc python3-statsmodels python-pil-doc python3-pil-dbg python3-setuptools python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python3-cryptography python3-openssl python3-socks dvipng python3-sphinx-rtd-theme python3-stemmer sphinx-doc texlive-plain-generic python3.8-venv python3.8-doc sgml-base-doc openssl-blacklist gv | postscript-viewer perl-tk xpdf | pdf-viewer xzdec texlive-fonts-recommended-doc texlive-latex-base-doc icc-profiles libfile-which-perl libspreadsheet-parseexcel-perl texlive-latex-extra-doc texlive-latex-recommended-doc texlive-pstricks dot2tex prerex ruby-tcltk | libtcltk-ruby texlive-pictures-doc vprerex Recommended packages: libomp-10-dev libfl-dev curl | wget | lynx libmagickcore-6.q16-6-extra ghostscript netpbm xpdf | pdf-viewer gv | postscript-viewer libarchive-cpio-perl libgdk-pixbuf2.0-bin libglib2.0-data xdg-user-dirs javascript-common krb5-locales gsfonts publicsuffix librsvg2-common libsasl2-modules libltdl-dev libmail-sendmail-perl logrotate python3-scipy python3-matplotlib python3-numexpr python3-tables python3-xlrd python3-openpyxl python3-xlwt python3-bs4 python3-html5lib python3-lxml python3-olefile lmodern dvisvgm tex-gyre tipa texlive-plain-generic ruby | ruby-interpreter tk libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev binfmt-support bison bsdmainutils clang-10 cmake cmake-data debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common doxygen dwz file flex fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern gettext gettext-base groff-base hicolor-icon-theme icu-devtools imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian latexmk libapache-pom-java libarchive-zip-perl libarchive13 libasn1-8-heimdal libblas3 libboost-atomic1.71-dev libboost-atomic1.71.0 libboost-chrono1.71-dev libboost-chrono1.71.0 libboost-date-time1.71-dev libboost-date-time1.71.0 libboost-dev libboost-iostreams-dev libboost-iostreams1.71-dev libboost-iostreams1.71.0 libboost-python-dev libboost-python1.71-dev libboost-python1.71.0 libboost-regex-dev libboost-regex1.71-dev libboost-regex1.71.0 libboost-serialization1.71-dev libboost-serialization1.71.0 libboost-system-dev libboost-system1.71-dev libboost-system1.71.0 libboost-thread-dev libboost-thread1.71-dev libboost-thread1.71.0 libboost1.71-dev libbrotli1 libbsd0 libcairo2 libclang-common-10-dev libclang-cpp10 libclang1-10 libcommons-logging-java libcommons-parent-java libcroco3 libcurl4 libdatrie1 libdebhelper-perl libedit2 libelf1 libexpat1 libexpat1-dev libffi-dev libfftw3-double3 libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfreetype6 libfribidi0 libgc1c2 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz-icu0 libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libice6 libicu-dev libicu66 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libjsoncpp1 libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libllvm10 liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-6 libmagickwand-6.q16-6 libmpdec2 libncurses-dev libnghttp2-14 libobjc-9-dev libobjc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpdfbox-java libpfm4 libpipeline1 libpixman-1-0 libpq-dev libpq5 libpsl5 libptexenc1 libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib librhash0 libroken18-heimdal librsvg2-2 librsvg2-bin librtmp1 libsasl2-2 libsasl2-modules-db libschroedinger-coordgenlibs-dev libschroedinger-coordgenlibs1 libschroedinger-maeparser-dev libschroedinger-maeparser1 libsigsegv2 libsm6 libsqlite3-dev libssh-4 libsub-override-perl libsynctex2 libteckit0 libtexlua53 libtexluajit2 libthai-data libthai0 libtiff5 libtinfo-dev libtool libuchardet0 libuv1 libwebp6 libwebpdemux2 libwebpmux3 libwind0-heimdal libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libyaml-0-2 libz3-4 libz3-dev libzzip-0-13 llvm-10 llvm-10-dev llvm-10-runtime llvm-10-tools m4 man-db mime-support netbase pandoc pandoc-data po-debconf postgresql-client-12 postgresql-client-common postgresql-common postgresql-server-dev-12 postgresql-server-dev-all preview-latex-style python-babel-localedata python3 python3-alabaster python3-babel python3-certifi python3-chardet python3-commonmark-bkrs python3-dateutil python3-dev python3-distutils python3-docutils python3-idna python3-imagesize python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pygments python3-pyparsing python3-recommonmark python3-requests python3-roman python3-six python3-sphinx python3-tz python3-urllib3 python3-yaml python3.8 python3.8-dev python3.8-minimal rapidjson-dev sbuild-build-depends-rdkit-dummy sgml-base shared-mime-info sphinx-common ssl-cert t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ucf x11-common xdg-utils xml-core zlib1g-dev 0 upgraded, 276 newly installed, 0 to remove and 0 not upgraded. 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http://ftpmaster.internal/ubuntu focal/main armhf libhx509-5-heimdal armhf 7.7.0+dfsg-1ubuntu1 [89.0 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main armhf libkrb5-26-heimdal armhf 7.7.0+dfsg-1ubuntu1 [170 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main armhf libheimntlm0-heimdal armhf 7.7.0+dfsg-1ubuntu1 [13.2 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main armhf libgssapi3-heimdal armhf 7.7.0+dfsg-1ubuntu1 [79.9 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2 [13.4 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main armhf libsasl2-2 armhf 2.1.27+dfsg-2 [42.7 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main armhf libldap-common all 2.4.49+dfsg-2ubuntu1 [17.3 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main armhf libldap-2.4-2 armhf 2.4.49+dfsg-2ubuntu1 [134 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main armhf libnghttp2-14 armhf 1.40.0-1build1 [67.8 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build1 [49.1 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main armhf libssh-4 armhf 0.9.3-2ubuntu2 [147 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main armhf libcurl4 armhf 7.68.0-1ubuntu1 [202 kB] Get:103 http://ftpmaster.internal/ubuntu focal/main armhf libjsoncpp1 armhf 1.7.4-3.1ubuntu2 [65.1 kB] Get:104 http://ftpmaster.internal/ubuntu focal/main armhf librhash0 armhf 1.3.9-1 [125 kB] Get:105 http://ftpmaster.internal/ubuntu focal/main armhf libuv1 armhf 1.34.2-1ubuntu1 [68.1 kB] Get:106 http://ftpmaster.internal/ubuntu focal/main armhf cmake armhf 3.16.3-1ubuntu1 [3014 kB] Get:107 http://ftpmaster.internal/ubuntu focal/main armhf libtool all 2.4.6-14 [161 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main armhf dh-autoreconf all 19 [16.1 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main armhf libdebhelper-perl all 12.10ubuntu1 [62.1 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main armhf libarchive-zip-perl all 1.67-2 [90.5 kB] Get:111 http://ftpmaster.internal/ubuntu focal/main armhf libsub-override-perl all 0.09-2 [9532 B] Get:112 http://ftpmaster.internal/ubuntu focal/main armhf libfile-stripnondeterminism-perl all 1.6.3-2 [16.0 kB] Get:113 http://ftpmaster.internal/ubuntu focal/main armhf dh-strip-nondeterminism all 1.6.3-2 [5228 B] Get:114 http://ftpmaster.internal/ubuntu focal/main armhf dwz armhf 0.13-5 [153 kB] Get:115 http://ftpmaster.internal/ubuntu focal/main armhf libcroco3 armhf 0.6.13-1 [70.5 kB] Get:116 http://ftpmaster.internal/ubuntu focal/main armhf gettext armhf 0.19.8.1-10build1 [835 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:118 http://ftpmaster.internal/ubuntu focal/main armhf po-debconf all 1.0.21 [233 kB] Get:119 http://ftpmaster.internal/ubuntu focal/main armhf debhelper all 12.10ubuntu1 [877 kB] Get:120 http://ftpmaster.internal/ubuntu focal/main armhf python3-lib2to3 all 3.8.2-1ubuntu1 [74.1 kB] Get:121 http://ftpmaster.internal/ubuntu focal/main armhf python3-distutils all 3.8.2-1ubuntu1 [140 kB] Get:122 http://ftpmaster.internal/ubuntu focal/universe armhf dh-python all 4.20191017ubuntu7 [87.1 kB] Get:123 http://ftpmaster.internal/ubuntu focal/main armhf xml-core all 0.18+nmu1 [21.6 kB] Get:124 http://ftpmaster.internal/ubuntu focal/main armhf docutils-common all 0.16+dfsg-2 [116 kB] Get:125 http://ftpmaster.internal/ubuntu focal/universe armhf libxapian30 armhf 1.4.14-2 [547 kB] Get:126 http://ftpmaster.internal/ubuntu focal/universe armhf doxygen armhf 1.8.17-0ubuntu2 [8164 kB] Get:127 http://ftpmaster.internal/ubuntu focal/main armhf fontconfig armhf 2.13.1-2ubuntu3 [170 kB] Get:128 http://ftpmaster.internal/ubuntu focal/universe armhf fonts-lmodern all 2.004.5-6 [4532 kB] Get:129 http://ftpmaster.internal/ubuntu focal/main armhf hicolor-icon-theme all 0.17-2 [9976 B] Get:130 http://ftpmaster.internal/ubuntu focal/main armhf icu-devtools armhf 66.1-2ubuntu2 [167 kB] Get:131 http://ftpmaster.internal/ubuntu focal/universe armhf imagemagick-6.q16 armhf 8:6.9.10.23+dfsg-2.1ubuntu11 [427 kB] Get:132 http://ftpmaster.internal/ubuntu focal/universe armhf imagemagick armhf 8:6.9.10.23+dfsg-2.1ubuntu11 [14.4 kB] Get:133 http://ftpmaster.internal/ubuntu focal/main armhf libpaper1 armhf 1.1.28 [12.1 kB] Get:134 http://ftpmaster.internal/ubuntu focal/main armhf libpaper-utils armhf 1.1.28 [7960 B] Get:135 http://ftpmaster.internal/ubuntu focal/main armhf libkpathsea6 armhf 2019.20190605.51237-3build2 [48.7 kB] Get:136 http://ftpmaster.internal/ubuntu focal/main armhf libptexenc1 armhf 2019.20190605.51237-3build2 [32.7 kB] Get:137 http://ftpmaster.internal/ubuntu focal/main armhf libsynctex2 armhf 2019.20190605.51237-3build2 [42.9 kB] Get:138 http://ftpmaster.internal/ubuntu focal/main armhf libtexlua53 armhf 2019.20190605.51237-3build2 [81.2 kB] Get:139 http://ftpmaster.internal/ubuntu focal/main armhf libtexluajit2 armhf 2019.20190605.51237-3build2 [181 kB] Get:140 http://ftpmaster.internal/ubuntu focal/main armhf t1utils armhf 1.41-3 [48.2 kB] Get:141 http://ftpmaster.internal/ubuntu focal/main armhf libpixman-1-0 armhf 0.38.4-0ubuntu1 [159 kB] Get:142 http://ftpmaster.internal/ubuntu focal/main armhf libxcb-render0 armhf 1.14-2 [14.2 kB] Get:143 http://ftpmaster.internal/ubuntu focal/main armhf libxcb-shm0 armhf 1.14-2 [5540 B] Get:144 http://ftpmaster.internal/ubuntu focal/main armhf libxrender1 armhf 1:0.9.10-1 [15.6 kB] Get:145 http://ftpmaster.internal/ubuntu focal/main armhf libcairo2 armhf 1.16.0-4ubuntu1 [503 kB] Get:146 http://ftpmaster.internal/ubuntu focal/main armhf libgraphite2-3 armhf 1.3.13-11build1 [62.7 kB] Get:147 http://ftpmaster.internal/ubuntu focal/main armhf libharfbuzz0b armhf 2.6.4-1ubuntu4 [347 kB] Get:148 http://ftpmaster.internal/ubuntu focal/main armhf libharfbuzz-icu0 armhf 2.6.4-1ubuntu4 [5032 B] Get:149 http://ftpmaster.internal/ubuntu focal/universe armhf libteckit0 armhf 2.5.8+ds2-5ubuntu2 [247 kB] Get:150 http://ftpmaster.internal/ubuntu focal/main armhf x11-common all 1:7.7+19ubuntu14 [22.3 kB] Get:151 http://ftpmaster.internal/ubuntu focal/main armhf libice6 armhf 2:1.0.10-0ubuntu1 [34.1 kB] Get:152 http://ftpmaster.internal/ubuntu focal/main armhf libsm6 armhf 2:1.2.3-1 [14.1 kB] Get:153 http://ftpmaster.internal/ubuntu focal/main armhf libxt6 armhf 1:1.1.5-1 [129 kB] Get:154 http://ftpmaster.internal/ubuntu focal/main armhf libxmu6 armhf 2:1.1.3-0ubuntu1 [38.3 kB] Get:155 http://ftpmaster.internal/ubuntu focal/main armhf libxpm4 armhf 1:3.5.12-1 [29.0 kB] Get:156 http://ftpmaster.internal/ubuntu focal/main armhf libxaw7 armhf 2:1.0.13-1 [141 kB] Get:157 http://ftpmaster.internal/ubuntu focal/main armhf libxi6 armhf 2:1.7.10-0ubuntu1 [25.0 kB] Get:158 http://ftpmaster.internal/ubuntu focal/universe armhf libzzip-0-13 armhf 0.13.62-3.2ubuntu1 [22.1 kB] Get:159 http://ftpmaster.internal/ubuntu focal/universe armhf texlive-binaries armhf 2019.20190605.51237-3build2 [6158 kB] Get:160 http://ftpmaster.internal/ubuntu focal/main armhf xdg-utils all 1.1.3-2ubuntu1 [61.6 kB] Get:161 http://ftpmaster.internal/ubuntu focal/universe armhf texlive-base all 2019.20200218-1 [20.8 MB] Get:162 http://ftpmaster.internal/ubuntu focal/universe armhf texlive-latex-base all 2019.20200218-1 [990 kB] Get:163 http://ftpmaster.internal/ubuntu focal/universe armhf latexmk all 1:4.67-0.1 [376 kB] Get:164 http://ftpmaster.internal/ubuntu focal/universe armhf libapache-pom-java all 18-1 [4720 B] Get:165 http://ftpmaster.internal/ubuntu focal/main armhf libblas3 armhf 3.9.0-1build1 [102 kB] Get:166 http://ftpmaster.internal/ubuntu focal/main armhf libboost1.71-dev armhf 1.71.0-6ubuntu6 [9068 kB] Get:167 http://ftpmaster.internal/ubuntu focal/main armhf libboost-atomic1.71.0 armhf 1.71.0-6ubuntu6 [205 kB] Get:168 http://ftpmaster.internal/ubuntu focal/main armhf libboost-atomic1.71-dev armhf 1.71.0-6ubuntu6 [205 kB] Get:169 http://ftpmaster.internal/ubuntu focal/main armhf libboost-chrono1.71.0 armhf 1.71.0-6ubuntu6 [213 kB] Get:170 http://ftpmaster.internal/ubuntu focal/main armhf libboost-chrono1.71-dev armhf 1.71.0-6ubuntu6 [220 kB] Get:171 http://ftpmaster.internal/ubuntu focal/main armhf libboost-date-time1.71.0 armhf 1.71.0-6ubuntu6 [216 kB] Get:172 http://ftpmaster.internal/ubuntu focal/main armhf libboost-serialization1.71.0 armhf 1.71.0-6ubuntu6 [283 kB] Get:173 http://ftpmaster.internal/ubuntu focal/main armhf libboost-serialization1.71-dev armhf 1.71.0-6ubuntu6 [356 kB] Get:174 http://ftpmaster.internal/ubuntu focal/main armhf libboost-date-time1.71-dev armhf 1.71.0-6ubuntu6 [229 kB] Get:175 http://ftpmaster.internal/ubuntu focal/main armhf libboost-dev armhf 1.71.0.0ubuntu1 [3600 B] Get:176 http://ftpmaster.internal/ubuntu focal/universe armhf libboost-regex1.71.0 armhf 1.71.0-6ubuntu6 [418 kB] Get:177 http://ftpmaster.internal/ubuntu focal/main armhf libicu-dev armhf 66.1-2ubuntu2 [9208 kB] Get:178 http://ftpmaster.internal/ubuntu focal/universe armhf libboost-regex1.71-dev armhf 1.71.0-6ubuntu6 [554 kB] Get:179 http://ftpmaster.internal/ubuntu focal/main armhf libboost-iostreams1.71.0 armhf 1.71.0-6ubuntu6 [230 kB] Get:180 http://ftpmaster.internal/ubuntu focal/universe armhf libboost-iostreams1.71-dev armhf 1.71.0-6ubuntu6 [246 kB] Get:181 http://ftpmaster.internal/ubuntu focal/universe armhf libboost-iostreams-dev armhf 1.71.0.0ubuntu1 [3380 B] Get:182 http://ftpmaster.internal/ubuntu focal/main armhf libboost-python1.71.0 armhf 1.71.0-6ubuntu6 [265 kB] Get:183 http://ftpmaster.internal/ubuntu focal/main armhf libpython3.8 armhf 3.8.2-1ubuntu1 [1394 kB] Get:184 http://ftpmaster.internal/ubuntu focal/main armhf libexpat1-dev armhf 2.2.9-1build1 [99.8 kB] Get:185 http://ftpmaster.internal/ubuntu focal/main armhf libpython3.8-dev armhf 3.8.2-1ubuntu1 [3134 kB] Get:186 http://ftpmaster.internal/ubuntu focal/main armhf libpython3-dev armhf 3.8.2-0ubuntu2 [7236 B] Get:187 http://ftpmaster.internal/ubuntu focal/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2ubuntu1 [150 kB] Get:188 http://ftpmaster.internal/ubuntu focal/main armhf python3.8-dev armhf 3.8.2-1ubuntu1 [515 kB] Get:189 http://ftpmaster.internal/ubuntu focal/main armhf python3-dev armhf 3.8.2-0ubuntu2 [1212 B] Get:190 http://ftpmaster.internal/ubuntu focal/universe armhf libboost-python1.71-dev armhf 1.71.0-6ubuntu6 [293 kB] Get:191 http://ftpmaster.internal/ubuntu focal/universe armhf libboost-python-dev armhf 1.71.0.0ubuntu1 [3692 B] Get:192 http://ftpmaster.internal/ubuntu focal/universe armhf libboost-regex-dev armhf 1.71.0.0ubuntu1 [3652 B] Get:193 http://ftpmaster.internal/ubuntu focal/main armhf libboost-system1.71.0 armhf 1.71.0-6ubuntu6 [205 kB] Get:194 http://ftpmaster.internal/ubuntu focal/main armhf libboost-system1.71-dev armhf 1.71.0-6ubuntu6 [205 kB] Get:195 http://ftpmaster.internal/ubuntu focal/main armhf libboost-system-dev armhf 1.71.0.0ubuntu1 [3536 B] Get:196 http://ftpmaster.internal/ubuntu focal/main armhf libboost-thread1.71.0 armhf 1.71.0-6ubuntu6 [239 kB] Get:197 http://ftpmaster.internal/ubuntu focal/main armhf libboost-thread1.71-dev armhf 1.71.0-6ubuntu6 [255 kB] Get:198 http://ftpmaster.internal/ubuntu focal/main armhf libboost-thread-dev armhf 1.71.0.0ubuntu1 [3424 B] Get:199 http://ftpmaster.internal/ubuntu focal/universe armhf libcommons-parent-java all 43-1 [10.8 kB] Get:200 http://ftpmaster.internal/ubuntu focal/universe armhf libcommons-logging-java all 1.2-2 [60.3 kB] Get:201 http://ftpmaster.internal/ubuntu focal/main armhf libdatrie1 armhf 0.2.12-3 [15.2 kB] Get:202 http://ftpmaster.internal/ubuntu focal/main armhf libgdk-pixbuf2.0-common all 2.40.0+dfsg-3 [4896 B] Get:203 http://ftpmaster.internal/ubuntu focal/main armhf libgdk-pixbuf2.0-0 armhf 2.40.0+dfsg-3 [152 kB] Get:204 http://ftpmaster.internal/ubuntu focal/main armhf libgfortran5 armhf 10-20200405-0ubuntu1 [249 kB] Get:205 http://ftpmaster.internal/ubuntu focal/main armhf libimagequant0 armhf 2.12.2-1.1 [26.2 kB] Get:206 http://ftpmaster.internal/ubuntu focal/main armhf libjs-jquery all 3.3.1~dfsg-3 [329 kB] Get:207 http://ftpmaster.internal/ubuntu focal/main armhf libjs-underscore all 1.9.1~dfsg-1 [98.6 kB] Get:208 http://ftpmaster.internal/ubuntu focal/main armhf libjs-sphinxdoc all 1.8.5-7ubuntu1 [97.0 kB] Get:209 http://ftpmaster.internal/ubuntu focal/main armhf liblapack3 armhf 3.9.0-1build1 [1733 kB] Get:210 http://ftpmaster.internal/ubuntu focal/main armhf libncurses-dev armhf 6.2-0ubuntu2 [301 kB] Get:211 http://ftpmaster.internal/ubuntu focal/main armhf libthai-data all 0.1.28-3 [134 kB] Get:212 http://ftpmaster.internal/ubuntu focal/main armhf libthai0 armhf 0.1.28-3 [14.7 kB] Get:213 http://ftpmaster.internal/ubuntu focal/main armhf libpango-1.0-0 armhf 1.44.7-2ubuntu2 [144 kB] Get:214 http://ftpmaster.internal/ubuntu focal/main armhf libpangoft2-1.0-0 armhf 1.44.7-2ubuntu2 [28.6 kB] Get:215 http://ftpmaster.internal/ubuntu focal/main armhf libpangocairo-1.0-0 armhf 1.44.7-2ubuntu2 [20.8 kB] Get:216 http://ftpmaster.internal/ubuntu focal/main armhf libpq5 armhf 12.2-4 [97.1 kB] Get:217 http://ftpmaster.internal/ubuntu focal/main armhf libpq-dev armhf 12.2-4 [124 kB] Get:218 http://ftpmaster.internal/ubuntu focal/main armhf librsvg2-2 armhf 2.48.2-1 [1147 kB] Get:219 http://ftpmaster.internal/ubuntu focal/universe armhf librsvg2-bin armhf 2.48.2-1 [13.7 kB] Get:220 http://ftpmaster.internal/ubuntu focal/universe armhf libschroedinger-maeparser1 armhf 1.2.2-1build1 [76.5 kB] Get:221 http://ftpmaster.internal/ubuntu focal/universe armhf libschroedinger-coordgenlibs1 armhf 1.3-1build1 [152 kB] Get:222 http://ftpmaster.internal/ubuntu focal/universe armhf libschroedinger-coordgenlibs-dev armhf 1.3-1build1 [28.8 kB] Get:223 http://ftpmaster.internal/ubuntu focal/universe armhf libschroedinger-maeparser-dev armhf 1.2.2-1build1 [12.0 kB] Get:224 http://ftpmaster.internal/ubuntu focal/main armhf libsqlite3-dev armhf 3.31.1-4 [631 kB] Get:225 http://ftpmaster.internal/ubuntu focal/main armhf libtinfo-dev armhf 6.2-0ubuntu2 [968 B] Get:226 http://ftpmaster.internal/ubuntu focal/main armhf libwebpdemux2 armhf 0.6.1-2 [8760 B] Get:227 http://ftpmaster.internal/ubuntu focal/universe armhf llvm-10-runtime armhf 1:10.0.0-2ubuntu2 [154 kB] Get:228 http://ftpmaster.internal/ubuntu focal/main armhf libpfm4 armhf 4.10.1+git20-g7700f49-2 [33.0 kB] Get:229 http://ftpmaster.internal/ubuntu focal/universe armhf llvm-10 armhf 1:10.0.0-2ubuntu2 [4147 kB] Get:230 http://ftpmaster.internal/ubuntu focal/main armhf libffi-dev armhf 3.3-4 [53.0 kB] Get:231 http://ftpmaster.internal/ubuntu focal/main armhf python3-pygments all 2.3.1+dfsg-1ubuntu2 [579 kB] Get:232 http://ftpmaster.internal/ubuntu focal/universe armhf llvm-10-tools armhf 1:10.0.0-2ubuntu2 [278 kB] Get:233 http://ftpmaster.internal/ubuntu focal/universe armhf libz3-4 armhf 4.8.7-4build1 [5781 kB] Get:234 http://ftpmaster.internal/ubuntu focal/universe armhf libz3-dev armhf 4.8.7-4build1 [67.5 kB] Get:235 http://ftpmaster.internal/ubuntu focal/universe armhf llvm-10-dev armhf 1:10.0.0-2ubuntu2 [25.5 MB] Get:236 http://ftpmaster.internal/ubuntu focal/universe armhf pandoc-data all 2.5-3build2 [76.0 kB] Get:237 http://ftpmaster.internal/ubuntu focal/universe armhf pandoc armhf 2.5-3build2 [18.3 MB] Get:238 http://ftpmaster.internal/ubuntu focal/main armhf postgresql-client-common all 214 [28.2 kB] Get:239 http://ftpmaster.internal/ubuntu focal/main armhf postgresql-client-12 armhf 12.2-4 [987 kB] Get:240 http://ftpmaster.internal/ubuntu focal/main armhf ssl-cert all 1.0.39 [17.0 kB] Get:241 http://ftpmaster.internal/ubuntu focal/main armhf postgresql-common all 214 [169 kB] Get:242 http://ftpmaster.internal/ubuntu focal/universe armhf postgresql-server-dev-12 armhf 12.2-4 [907 kB] Get:243 http://ftpmaster.internal/ubuntu focal/universe armhf postgresql-server-dev-all all 214 [7692 B] Get:244 http://ftpmaster.internal/ubuntu focal/universe armhf preview-latex-style all 11.91-2ubuntu2 [184 kB] Get:245 http://ftpmaster.internal/ubuntu focal/main armhf python-babel-localedata all 2.6.0+dfsg.1-1ubuntu2 [4627 kB] Get:246 http://ftpmaster.internal/ubuntu focal/main armhf python3-tz all 2019.3-1 [24.4 kB] Get:247 http://ftpmaster.internal/ubuntu focal/main armhf python3-babel all 2.6.0+dfsg.1-1ubuntu2 [83.5 kB] Get:248 http://ftpmaster.internal/ubuntu focal/main armhf python3-certifi all 2019.11.28-1 [149 kB] Get:249 http://ftpmaster.internal/ubuntu focal/main armhf python3-chardet all 3.0.4-4build1 [80.4 kB] Get:250 http://ftpmaster.internal/ubuntu focal/universe armhf python3-commonmark-bkrs all 0.5.4+ds-4 [29.6 kB] Get:251 http://ftpmaster.internal/ubuntu focal/main armhf python3-dateutil all 2.7.3-3ubuntu1 [63.3 kB] Get:252 http://ftpmaster.internal/ubuntu focal/main armhf python3-roman all 2.0.0-3build1 [8728 B] Get:253 http://ftpmaster.internal/ubuntu focal/main armhf python3-docutils all 0.16+dfsg-2 [368 kB] Get:254 http://ftpmaster.internal/ubuntu focal/main armhf python3-idna all 2.8-1 [34.6 kB] Get:255 http://ftpmaster.internal/ubuntu focal/universe armhf python3-imagesize all 1.2.0-1 [5808 B] Get:256 http://ftpmaster.internal/ubuntu focal/main armhf python3-markupsafe armhf 1.1.0-1build2 [13.3 kB] Get:257 http://ftpmaster.internal/ubuntu focal/main armhf python3-jinja2 all 2.10.1-2 [95.5 kB] Get:258 http://ftpmaster.internal/ubuntu focal/main armhf python3-numpy armhf 1:1.17.4-5ubuntu3 [3034 kB] Get:259 http://ftpmaster.internal/ubuntu focal/main armhf python3-pyparsing all 2.4.6-1 [61.3 kB] Get:260 http://ftpmaster.internal/ubuntu focal/main armhf python3-packaging all 20.3-1 [26.8 kB] Get:261 http://ftpmaster.internal/ubuntu focal/universe armhf python3-pandas-lib armhf 0.25.3+dfsg-7 [4097 kB] Get:262 http://ftpmaster.internal/ubuntu focal/universe armhf python3-pandas all 0.25.3+dfsg-7 [1968 kB] Get:263 http://ftpmaster.internal/ubuntu focal/main armhf python3-pil armhf 7.0.0-4build1 [337 kB] Get:264 http://ftpmaster.internal/ubuntu focal/universe armhf python3-recommonmark all 0.4.0+ds-6 [15.0 kB] Get:265 http://ftpmaster.internal/ubuntu focal/main armhf python3-urllib3 all 1.25.8-1 [88.5 kB] Get:266 http://ftpmaster.internal/ubuntu focal/main armhf python3-requests all 2.22.0-2build1 [46.7 kB] Get:267 http://ftpmaster.internal/ubuntu focal/universe armhf sphinx-common all 1.8.5-7ubuntu1 [492 kB] Get:268 http://ftpmaster.internal/ubuntu focal/universe armhf python3-alabaster all 0.7.8-1build1 [18.7 kB] Get:269 http://ftpmaster.internal/ubuntu focal/universe armhf python3-sphinx all 1.8.5-7ubuntu1 [482 kB] Get:270 http://ftpmaster.internal/ubuntu focal/universe armhf rapidjson-dev all 1.1.0+dfsg2-5ubuntu1 [95.0 kB] Get:271 http://ftpmaster.internal/ubuntu focal/universe armhf texlive-fonts-recommended all 2019.20200218-1 [4972 kB] Get:272 http://ftpmaster.internal/ubuntu focal/universe armhf libfontbox-java all 1:1.8.16-2 [207 kB] Get:273 http://ftpmaster.internal/ubuntu focal/universe armhf libpdfbox-java all 1:1.8.16-2 [5199 kB] Get:274 http://ftpmaster.internal/ubuntu focal/universe armhf texlive-latex-recommended all 2019.20200218-1 [15.7 MB] Get:275 http://ftpmaster.internal/ubuntu focal/universe armhf texlive-pictures all 2019.20200218-1 [4492 kB] Get:276 http://ftpmaster.internal/ubuntu focal/universe armhf texlive-latex-extra all 2019.202000218-1 [12.5 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 261 MB in 24s (10.7 MB/s) Selecting previously unselected package libpython3.8-minimal:armhf. (Reading database ... 12562 files and directories currently installed.) Preparing to unpack .../libpython3.8-minimal_3.8.2-1ubuntu1_armhf.deb ... Unpacking libpython3.8-minimal:armhf (3.8.2-1ubuntu1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.2.9-1build1_armhf.deb ... Unpacking libexpat1:armhf (2.2.9-1build1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.2-1ubuntu1_armhf.deb ... Unpacking python3.8-minimal (3.8.2-1ubuntu1) ... Setting up libpython3.8-minimal:armhf (3.8.2-1ubuntu1) ... Setting up libexpat1:armhf (2.2.9-1build1) ... Setting up python3.8-minimal (3.8.2-1ubuntu1) ... Selecting previously unselected package python3-minimal. (Reading database ... 12853 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.2-0ubuntu2_armhf.deb ... Unpacking python3-minimal (3.8.2-0ubuntu2) ... 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No schema files found: doing nothing. Setting up libicu66:armhf (66.1-2ubuntu2) ... Setting up libtexluajit2:armhf (2019.20190605.51237-3build2) ... Setting up libdebhelper-perl (12.10ubuntu1) ... Setting up libbrotli1:armhf (1.0.7-6build1) ... Setting up libfontbox-java (1:1.8.16-2) ... Setting up libboost1.71-dev:armhf (1.71.0-6ubuntu6) ... Setting up libboost-chrono1.71.0:armhf (1.71.0-6ubuntu6) ... Setting up libgdk-pixbuf2.0-common (2.40.0+dfsg-3) ... Setting up x11-common (1:7.7+19ubuntu14) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:armhf (1.40.0-1build1) ... Setting up libmagic1:armhf (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up libobjc4:armhf (10-20200405-0ubuntu1) ... Setting up libzzip-0-13:armhf (0.13.62-3.2ubuntu1) ... Setting up file (1:5.38-4) ... 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Setting up libwebp6:armhf (0.6.1-2) ... Setting up icu-devtools (66.1-2ubuntu2) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libboost-regex1.71.0:armhf (1.71.0-6ubuntu6) ... Setting up ucf (3.0038+nmu1) ... Setting up libk5crypto3:armhf (1.17-6ubuntu4) ... Setting up libjpeg-turbo8:armhf (2.0.3-0ubuntu1) ... Setting up libobjc-9-dev:armhf (9.3.0-10ubuntu1) ... Setting up libltdl7:armhf (2.4.6-14) ... Setting up libfftw3-double3:armhf (3.3.8-2ubuntu1) ... Setting up libkpathsea6:armhf (2019.20190605.51237-3build2) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2) ... Setting up libgfortran5:armhf (10-20200405-0ubuntu1) ... Setting up libroken18-heimdal:armhf (7.7.0+dfsg-1ubuntu1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2ubuntu1) ... Setting up liblqr-1-0:armhf (0.4.2-2.1) ... Setting up librhash0:armhf (1.3.9-1) ... Setting up libuchardet0:armhf (0.0.6-3build1) ... Setting up libboost-thread1.71.0:armhf (1.71.0-6ubuntu6) ... Setting up fonts-lmodern (2.004.5-6) ... 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Setting up liblapack3:armhf (3.9.0-1build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libxcb1:armhf (1.14-2) ... Setting up libharfbuzz-icu0:armhf (2.6.4-1ubuntu4) ... Setting up libpdfbox-java (1:1.8.16-2) ... Setting up libtool (2.4.6-14) ... Setting up libarchive13:armhf (3.4.0-2ubuntu1) ... Setting up libxcb-render0:armhf (1.14-2) ... Setting up fontconfig-config (2.13.1-2ubuntu3) ... Setting up libwebpdemux2:armhf (0.6.1-2) ... Setting up libasn1-8-heimdal:armhf (7.7.0+dfsg-1ubuntu1) ... Setting up libedit2:armhf (3.1-20191231-1) ... Setting up libcommons-parent-java (43-1) ... Setting up libcommons-logging-java (1.2-2) ... Setting up m4 (1.4.18-4) ... Setting up libschroedinger-coordgenlibs1:armhf (1.3-1build1) ... Setting up python3 (3.8.2-0ubuntu2) ... Setting up libxcb-shm0:armhf (1.14-2) ... Setting up libpaper-utils (1.1.28) ... Setting up python3-markupsafe (1.1.0-1build2) ... Setting up libhcrypto4-heimdal:armhf (7.7.0+dfsg-1ubuntu1) ... Setting up python3-tz (2019.3-1) ... Setting up libboost-system1.71-dev:armhf (1.71.0-6ubuntu6) ... Setting up libllvm10:armhf (1:10.0.0-2ubuntu2) ... Setting up python3-six (1.14.0-2) ... Setting up tex-common (6.13) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libthai0:armhf (0.1.28-3) ... Setting up python3-roman (2.0.0-3build1) ... Setting up libwind0-heimdal:armhf (7.7.0+dfsg-1ubuntu1) ... Setting up python3-jinja2 (2.10.1-2) ... Setting up python3-pygments (2.3.1+dfsg-1ubuntu2) ... Setting up libptexenc1:armhf (2019.20190605.51237-3build2) ... Setting up pandoc (2.5-3build2) ... Setting up python3-pyparsing (2.4.6-1) ... Setting up python3-certifi (2019.11.28-1) ... Setting up libclang1-10 (1:10.0.0-2ubuntu2) ... Setting up libpython3.8:armhf (3.8.2-1ubuntu1) ... Setting up shared-mime-info (1.15-1) ... Setting up bsdmainutils (11.1.2ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up postgresql-common (214) ... Adding user postgres to group ssl-cert Creating config file /etc/postgresql-common/createcluster.conf with new version Building PostgreSQL dictionaries from installed myspell/hunspell packages... Removing obsolete dictionary files: Created symlink /etc/systemd/system/multi-user.target.wants/postgresql.service → /lib/systemd/system/postgresql.service. Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libgssapi-krb5-2:armhf (1.17-6ubuntu4) ... Setting up python3-idna (2.8-1) ... Setting up libboost-regex1.71-dev:armhf (1.71.0-6ubuntu6) ... Setting up libcroco3:armhf (0.6.13-1) ... Setting up libboost-serialization1.71-dev:armhf (1.71.0-6ubuntu6) ... Setting up libjs-sphinxdoc (1.8.5-7ubuntu1) ... Setting up libssh-4:armhf (0.9.3-2ubuntu2) ... Setting up autoconf (2.69-11.1) ... Setting up python3-urllib3 (1.25.8-1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up libboost-date-time1.71-dev:armhf (1.71.0-6ubuntu6) ... Setting up python3-commonmark-bkrs (0.5.4+ds-4) ... Setting up groff-base (1.22.4-4build1) ... Setting up xml-core (0.18+nmu1) ... Setting up bison (2:3.5.1+dfsg-1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libx11-6:armhf (2:1.6.9-2ubuntu1) ... Setting up python3-dateutil (2.7.3-3ubuntu1) ... Setting up libtiff5:armhf (4.1.0+git191117-2build1) ... Setting up libfontconfig1:armhf (2.13.1-2ubuntu3) ... Setting up libboost-regex-dev:armhf (1.71.0.0ubuntu1) ... Setting up python3-lib2to3 (3.8.2-1ubuntu1) ... Setting up libsm6:armhf (2:1.2.3-1) ... Setting up libboost-iostreams1.71-dev:armhf (1.71.0-6ubuntu6) ... Setting up python3-imagesize (1.2.0-1) ... Setting up python3-pkg-resources (45.2.0-1) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3-distutils (3.8.2-1ubuntu1) ... Setting up dh-python (4.20191017ubuntu7) ... Setting up fontconfig (2.13.1-2ubuntu3) ... Regenerating fonts cache... done. Setting up flex (2.6.4-6.2) ... Setting up gettext (0.19.8.1-10build1) ... Setting up libxpm4:armhf (1:3.5.12-1) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up python3-babel (2.6.0+dfsg.1-1ubuntu2) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up libschroedinger-coordgenlibs-dev:armhf (1.3-1build1) ... Setting up libclang-common-10-dev (1:10.0.0-2ubuntu2) ... Setting up python3-alabaster (0.7.8-1build1) ... Setting up libhx509-5-heimdal:armhf (7.7.0+dfsg-1ubuntu1) ... Setting up preview-latex-style (11.91-2ubuntu2) ... Setting up libboost-thread1.71-dev:armhf (1.71.0-6ubuntu6) ... Setting up libboost-system-dev:armhf (1.71.0.0ubuntu1) ... Setting up libpango-1.0-0:armhf (1.44.7-2ubuntu2) ... Setting up libxext6:armhf (2:1.3.4-0ubuntu1) ... Setting up python3-yaml (5.3.1-1) ... Setting up libboost-iostreams-dev:armhf (1.71.0.0ubuntu1) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libclang-cpp10 (1:10.0.0-2ubuntu2) ... Setting up libcairo2:armhf (1.16.0-4ubuntu1) ... Setting up llvm-10-runtime (1:10.0.0-2ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-pil:armhf (7.0.0-4build1) ... Setting up libmagickcore-6.q16-6:armhf (8:6.9.10.23+dfsg-2.1ubuntu11) ... Setting up doxygen (1.8.17-0ubuntu2) ... Setting up python3-packaging (20.3-1) ... Setting up python3-chardet (3.0.4-4build1) ... Setting up libpython3.8-dev:armhf (3.8.2-1ubuntu1) ... Setting up libgdk-pixbuf2.0-0:armhf (2.40.0+dfsg-3) ... Setting up sphinx-common (1.8.5-7ubuntu1) ... Setting up python3-requests (2.22.0-2build1) ... Setting up libxt6:armhf (1:1.1.5-1) ... Setting up python3-numpy (1:1.17.4-5ubuntu3) ... Setting up python3.8-dev (3.8.2-1ubuntu1) ... Setting up libmagickwand-6.q16-6:armhf (8:6.9.10.23+dfsg-2.1ubuntu11) ... Setting up clang-10 (1:10.0.0-2ubuntu2) ... Setting up libpangoft2-1.0-0:armhf (1.44.7-2ubuntu2) ... Setting up libboost-thread-dev:armhf (1.71.0.0ubuntu1) ... Setting up libpangocairo-1.0-0:armhf (1.44.7-2ubuntu2) ... Setting up libkrb5-26-heimdal:armhf (7.7.0+dfsg-1ubuntu1) ... Setting up libxmu6:armhf (2:1.1.3-0ubuntu1) ... Setting up llvm-10-tools (1:10.0.0-2ubuntu2) ... Setting up libpython3-dev:armhf (3.8.2-0ubuntu2) ... Setting up libxi6:armhf (2:1.7.10-0ubuntu1) ... Setting up po-debconf (1.0.21) ... Setting up python3-pandas-lib (0.25.3+dfsg-7) ... Setting up llvm-10 (1:10.0.0-2ubuntu2) ... Setting up libxaw7:armhf (2:1.0.13-1) ... Setting up libheimntlm0-heimdal:armhf (7.7.0+dfsg-1ubuntu1) ... Setting up librsvg2-2:armhf (2.48.2-1) ... Setting up llvm-10-dev (1:10.0.0-2ubuntu2) ... Setting up python3-pandas (0.25.3+dfsg-7) ... /usr/lib/python3/dist-packages/pandas/tests/frame/test_alter_axes.py:241: SyntaxWarning: "is" with a literal. Did you mean "=="? False if (keys[0] is "A" and keys[1] is "A") else drop # noqa: F632 /usr/lib/python3/dist-packages/pandas/tests/frame/test_alter_axes.py:241: SyntaxWarning: "is" with a literal. Did you mean "=="? False if (keys[0] is "A" and keys[1] is "A") else drop # noqa: F632 Setting up libgssapi3-heimdal:armhf (7.7.0+dfsg-1ubuntu1) ... Setting up python3-dev (3.8.2-0ubuntu2) ... Setting up imagemagick-6.q16 (8:6.9.10.23+dfsg-2.1ubuntu11) ... update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode Setting up texlive-binaries (2019.20190605.51237-3build2) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2019.20200218-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex Setting up librsvg2-bin (2.48.2-1) ... Setting up libboost-python1.71-dev (1.71.0-6ubuntu6) ... Setting up libldap-2.4-2:armhf (2.4.49+dfsg-2ubuntu1) ... Setting up libboost-python-dev (1.71.0.0ubuntu1) ... Setting up texlive-latex-base (2019.20200218-1) ... Setting up texlive-latex-recommended (2019.20200218-1) ... Setting up texlive-pictures (2019.20200218-1) ... Setting up imagemagick (8:6.9.10.23+dfsg-2.1ubuntu11) ... Setting up texlive-fonts-recommended (2019.20200218-1) ... Setting up libcurl4:armhf (7.68.0-1ubuntu1) ... Setting up libpq5:armhf (12.2-4) ... Setting up latexmk (1:4.67-0.1) ... Setting up texlive-latex-extra (2019.202000218-1) ... Setting up libpq-dev (12.2-4) ... Setting up postgresql-client-12 (12.2-4) ... update-alternatives: using /usr/share/postgresql/12/man/man1/psql.1.gz to provide /usr/share/man/man1/psql.1.gz (psql.1.gz) in auto mode Setting up cmake (3.16.3-1ubuntu1) ... Setting up postgresql-server-dev-12 (12.2-4) ... Setting up postgresql-server-dev-all (214) ... Setting up debhelper (12.10ubuntu1) ... Setting up dh-autoreconf (19) ... Processing triggers for libc-bin (2.31-0ubuntu7) ... Processing triggers for systemd (245.4-2ubuntu1) ... Processing triggers for sgml-base (1.29.1) ... Setting up docutils-common (0.16+dfsg-2) ... Processing triggers for sgml-base (1.29.1) ... Setting up python3-docutils (0.16+dfsg-2) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-recommonmark (0.4.0+ds-6) ... Setting up python3-sphinx (1.8.5-7ubuntu1) ... update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-apidoc to provide /usr/bin/sphinx-apidoc (sphinx-apidoc) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-autogen to provide /usr/bin/sphinx-autogen (sphinx-autogen) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-build to provide /usr/bin/sphinx-build (sphinx-build) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-quickstart to provide /usr/bin/sphinx-quickstart (sphinx-quickstart) in auto mode Setting up sbuild-build-depends-rdkit-dummy (0.invalid.0) ... Processing triggers for tex-common (6.13) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-177-generic arm64 (armv7l) Toolchain package versions: binutils_2.34-6ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-10ubuntu1 gcc-9_9.3.0-10ubuntu1 libc6-dev_2.31-0ubuntu7 libstdc++-9-dev_9.3.0-10ubuntu1 libstdc++6_10-20200405-0ubuntu1 linux-libc-dev_5.4.0-21.25 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1build1 apt_2.0.1ubuntu1 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu4 base-passwd_3.5.47 bash_5.0-6ubuntu1 binfmt-support_2.2.0-2 binutils_2.34-6ubuntu1 binutils-arm-linux-gnueabihf_2.34-6ubuntu1 binutils-common_2.34-6ubuntu1 bison_2:3.5.1+dfsg-1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.34-0.1ubuntu9 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110ubuntu1 clang-10_1:10.0.0-2ubuntu2 cmake_3.16.3-1ubuntu1 cmake-data_3.16.3-1ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-10ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.10ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20191017ubuntu7 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 docutils-common_0.16+dfsg-2 doxygen_1.8.17-0ubuntu2 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.5-2ubuntu1 fakeroot_1.24-1 fdisk_2.34-0.1ubuntu9 file_1:5.38-4 findutils_4.7.0-1ubuntu1 flex_2.6.4-6.2 fontconfig_2.13.1-2ubuntu3 fontconfig-config_2.13.1-2ubuntu3 fonts-dejavu-core_2.37-1 fonts-lmodern_2.004.5-6 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-10ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10-20200405-0ubuntu1 gcc-9_9.3.0-10ubuntu1 gcc-9-base_9.3.0-10ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.19-3ubuntu2 gpg-agent_2.2.19-3ubuntu2 gpgconf_2.2.19-3ubuntu2 gpgv_2.2.19-3ubuntu2 grep_3.4-1 groff-base_1.22.4-4build1 gzip_1.10-0ubuntu4 hicolor-icon-theme_0.17-2 hostname_3.23 icu-devtools_66.1-2ubuntu2 imagemagick_8:6.9.10.23+dfsg-2.1ubuntu11 imagemagick-6-common_8:6.9.10.23+dfsg-2.1ubuntu11 imagemagick-6.q16_8:6.9.10.23+dfsg-2.1ubuntu11 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 latexmk_1:4.67-0.1 libacl1_2.2.53-6 libapache-pom-java_18-1 libapparmor1_2.13.3-7ubuntu4 libapt-pkg6.0_2.0.1ubuntu1 libarchive-zip-perl_1.67-2 libarchive13_3.4.0-2ubuntu1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-10ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-1ubuntu1 libassuan0_2.5.3-7ubuntu2 libatomic1_10-20200405-0ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.34-6ubuntu1 libblas3_3.9.0-1build1 libblkid1_2.34-0.1ubuntu9 libboost-atomic1.71-dev_1.71.0-6ubuntu6 libboost-atomic1.71.0_1.71.0-6ubuntu6 libboost-chrono1.71-dev_1.71.0-6ubuntu6 libboost-chrono1.71.0_1.71.0-6ubuntu6 libboost-date-time1.71-dev_1.71.0-6ubuntu6 libboost-date-time1.71.0_1.71.0-6ubuntu6 libboost-dev_1.71.0.0ubuntu1 libboost-iostreams-dev_1.71.0.0ubuntu1 libboost-iostreams1.71-dev_1.71.0-6ubuntu6 libboost-iostreams1.71.0_1.71.0-6ubuntu6 libboost-python-dev_1.71.0.0ubuntu1 libboost-python1.71-dev_1.71.0-6ubuntu6 libboost-python1.71.0_1.71.0-6ubuntu6 libboost-regex-dev_1.71.0.0ubuntu1 libboost-regex1.71-dev_1.71.0-6ubuntu6 libboost-regex1.71.0_1.71.0-6ubuntu6 libboost-serialization1.71-dev_1.71.0-6ubuntu6 libboost-serialization1.71.0_1.71.0-6ubuntu6 libboost-system-dev_1.71.0.0ubuntu1 libboost-system1.71-dev_1.71.0-6ubuntu6 libboost-system1.71.0_1.71.0-6ubuntu6 libboost-thread-dev_1.71.0.0ubuntu1 libboost-thread1.71-dev_1.71.0-6ubuntu6 libboost-thread1.71.0_1.71.0-6ubuntu6 libboost1.71-dev_1.71.0-6ubuntu6 libbrotli1_1.0.7-6build1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.31-0ubuntu7 libc-dev-bin_2.31-0ubuntu7 libc6_2.31-0ubuntu7 libc6-dev_2.31-0ubuntu7 libcairo2_1.16.0-4ubuntu1 libcap-ng0_0.7.9-2.1build1 libcap2_1:2.32-1 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python3-docutils_0.16+dfsg-2 python3-idna_2.8-1 python3-imagesize_1.2.0-1 python3-jinja2_2.10.1-2 python3-lib2to3_3.8.2-1ubuntu1 python3-markupsafe_1.1.0-1build2 python3-minimal_3.8.2-0ubuntu2 python3-numpy_1:1.17.4-5ubuntu3 python3-packaging_20.3-1 python3-pandas_0.25.3+dfsg-7 python3-pandas-lib_0.25.3+dfsg-7 python3-pil_7.0.0-4build1 python3-pkg-resources_45.2.0-1 python3-pygments_2.3.1+dfsg-1ubuntu2 python3-pyparsing_2.4.6-1 python3-recommonmark_0.4.0+ds-6 python3-requests_2.22.0-2build1 python3-roman_2.0.0-3build1 python3-six_1.14.0-2 python3-sphinx_1.8.5-7ubuntu1 python3-tz_2019.3-1 python3-urllib3_1.25.8-1 python3-yaml_5.3.1-1 python3.8_3.8.2-1ubuntu1 python3.8-dev_3.8.2-1ubuntu1 python3.8-minimal_3.8.2-1ubuntu1 rapidjson-dev_1.1.0+dfsg2-5ubuntu1 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-rdkit-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sgml-base_1.29.1 shared-mime-info_1.15-1 sphinx-common_1.8.5-7ubuntu1 ssl-cert_1.0.39 systemd_245.4-2ubuntu1 systemd-sysv_245.4-2ubuntu1 systemd-timesyncd_245.4-2ubuntu1 sysvinit-utils_2.96-2.1ubuntu1 t1utils_1.41-3 tar_1.30+dfsg-7 tex-common_6.13 texlive-base_2019.20200218-1 texlive-binaries_2019.20190605.51237-3build2 texlive-fonts-recommended_2019.20200218-1 texlive-latex-base_2019.20200218-1 texlive-latex-extra_2019.202000218-1 texlive-latex-recommended_2019.20200218-1 texlive-pictures_2019.20200218-1 tzdata_2019c-3ubuntu1 ubuntu-keyring_2020.02.11.1 ucf_3.0038+nmu1 util-linux_2.34-0.1ubuntu9 x11-common_1:7.7+19ubuntu14 xdg-utils_1.1.3-2ubuntu1 xml-core_0.18+nmu1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Mar 5 08:07:22 2020 UTC gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 gpgv: issuer "doko@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rdkit_201909.1-2ubuntu5.dsc dpkg-source: info: extracting rdkit in rdkit-201909.1 dpkg-source: info: unpacking rdkit_201909.1.orig.tar.xz dpkg-source: info: unpacking rdkit_201909.1-2ubuntu5.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 fix-ftbfs.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-18968999 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18968999 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18968999 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 201909.1-2ubuntu5 dpkg-buildpackage: info: source distribution focal dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean pg_buildext checkcontrol dh clean --with python3 --buildsystem=cmake --parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' find /<> -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 pg_buildext clean /<>/Code/PgSQL/rdkit build-%v ### clean 12 ### make[1]: Leaving directory '/<>' dh_clean -O--buildsystem=cmake -O--parallel debian/rules build-arch dh build-arch --with python3 --buildsystem=cmake --parallel dh_update_autotools_config -a -O--buildsystem=cmake -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' 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_NATIVE=OFF -DRDK_USE_URF=OFF -DCMAKE_INSTALL_PREFIX=/usr -DPYTHON_EXECUTABLE=/usr/bin/python3.8 ../ cd obj-arm-linux-gnueabihf && 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_AUTOGEN_VERBOSE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -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_NATIVE=OFF -DRDK_USE_URF=OFF -DCMAKE_INSTALL_PREFIX=/usr -DPYTHON_EXECUTABLE=/usr/bin/python3.8 ../ .. -- The C compiler identification is GNU 9.3.0 -- The CXX compiler identification is GNU 9.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- 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 -- Using unsigned short -- Check if the system is big endian - little endian -- Found Catch2 source in /<>/External/catch/catch CATCH: /<>/External/catch/catch/single_include -- Found Boost: /usr/lib/arm-linux-gnueabihf/cmake/Boost-1.71.0/BoostConfig.cmake (found suitable version "1.71.0", minimum required is "1.56.0") found components: python system serialization iostreams regex -- Found PythonInterp: /usr/bin/python3.8 (found version "3.8.2") -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.8.so (found version "3.8.2") 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,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "2.91.0") Eigen3 not found, disabling the Descriptors3D build. -- 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 == Using strict rotor definition -- maeparser include dir set as '/usr/include' -- maeparser libraries set as '/usr/lib/arm-linux-gnueabihf/libmaeparser.so' -- Found maeparser: /usr/include -- coordgen include dir set as /usr/include -- coordgen libraries set as '/usr/lib/arm-linux-gnueabihf/libcoordgen.so' -- Found coordgen: /usr/include == Updating Filters.cpp from pains file == Done updating pains files -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_AUTOGEN_VERBOSE CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/obj-arm-linux-gnueabihf make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build cd obj-arm-linux-gnueabihf && make -j4 make[2]: Entering directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<> -B/<>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles /<>/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends 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-DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/RDGeneral/types.cpp [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o cd /<>/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -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 /<>/Code/ML/Cluster/Murtagh/hc.c [ 0%] Building CXX object Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/RDStreams && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDStreams_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/RDStreams/streams.cpp [ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/RDGeneral/Invariant.cpp [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /<>/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -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 /<>/Code/ML/Cluster/Murtagh/hcdriver.c [ 1%] Linking C shared library ../../../../lib/libRDKithc.so cd /<>/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2019.09.1 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o cd /<>/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2019.09.1 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 1%] Built target hc [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/RDGeneral/utils.cpp [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/RDGeneral/RDLog.cpp [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Dict.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/Dict.cpp.o -c /<>/Code/RDGeneral/Dict.cpp [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/RDGeneral/LocaleSwitcher.cpp [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/RDGeneral/versions.cpp [ 2%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /<>/obj-arm-linux-gnueabihf/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2019.09.1 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 cd /<>/obj-arm-linux-gnueabihf/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2019.09.1 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 2%] Built target RDStreams [ 2%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so cd /<>/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2019.09.1 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/Dict.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeneral.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1 ../../lib/libRDKitRDGeneral.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 2%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/DataStructs /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/DataStructs /<>/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= 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[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Numerics/EigenSolvers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers /<>/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/RDBoost /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/RDBoost /<>/obj-arm-linux-gnueabihf/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= Scanning dependencies of target DataStructs make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/RDGeneral /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/RDGeneral /<>/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/BitVect.cpp Scanning dependencies of target RDBoost Scanning dependencies of target testRDValue make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build Scanning dependencies of target EigenSolvers make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 2%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp [ 2%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/RDBoost/Wrap.cpp [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/RDGeneral/testRDValue.cpp [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/SparseBitVect.cpp [ 2%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 2%] Built target EigenSolvers [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/ExplicitBitVect.cpp [ 2%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /<>/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2019.09.1 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2019.09.1 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 2%] Built target RDBoost In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/RDValue-taggedunion.h:40, from /<>/Code/RDGeneral/RDValue.h:39, from /<>/Code/RDGeneral/testRDValue.cpp:2: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/Utils.cpp /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/RDValue-taggedunion.h:40, from /<>/Code/RDGeneral/RDValue.h:39, from /<>/Code/RDGeneral/testRDValue.cpp:2: /usr/include/c++/9/bits/stl_vector.h: In function ‘void testVector() [with T = double]’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/base64.cpp.o -c /<>/Code/DataStructs/base64.cpp [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/BitOps.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/RDValue-taggedunion.h:40, from /<>/Code/RDGeneral/RDValue.h:39, from /<>/Code/RDGeneral/testRDValue.cpp:2: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/RDValue-taggedunion.h:40, from /<>/Code/RDGeneral/RDValue.h:39, from /<>/Code/RDGeneral/testRDValue.cpp:2: /usr/include/c++/9/bits/stl_vector.h: In function ‘void testVector() [with T = long double]’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/RDValue-taggedunion.h:40, from /<>/Code/RDGeneral/RDValue.h:39, from /<>/Code/RDGeneral/testRDValue.cpp:2: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/RDGeneral /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/RDGeneral /<>/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/DiscreteDistMat.cpp Scanning dependencies of target testDict make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 4%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/RDGeneral/testDict.cpp [ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /<>/Code/DataStructs/DiscreteValueVect.cpp [ 4%] Linking CXX executable testRDValue cd /<>/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 4%] Built target testRDValue make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/RDBoost/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap /<>/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= Scanning dependencies of target rdBase make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 4%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/RDBoost/Wrap/RDBase.cpp [ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/FPBReader.cpp [ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/MultiFPBReader.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/testDict.cpp:14: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘void testVectToString()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:26, from /usr/include/boost/dynamic_bitset.hpp:15, from /<>/Code/DataStructs/ExplicitBitVect.h:16, from /<>/Code/DataStructs/FPBReader.cpp:15: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from /usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:25, from /usr/include/boost/dynamic_bitset.hpp:15, from /<>/Code/DataStructs/ExplicitBitVect.h:16, from /<>/Code/DataStructs/FPBReader.cpp:15: /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1879 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from /usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:25, from /usr/include/boost/dynamic_bitset.hpp:15, from /<>/Code/DataStructs/ExplicitBitVect.h:16, from /<>/Code/DataStructs/FPBReader.cpp:15: /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from /usr/include/boost/core/swap.hpp:27, from /usr/include/boost/utility/swap.hpp:15, from /usr/include/boost/tuple/detail/tuple_basic.hpp:40, from /usr/include/boost/tuple/tuple.hpp:28, from /usr/include/boost/tuple/tuple_comparison.hpp:19, from /<>/Code/DataStructs/MultiFPBReader.cpp:11: /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from /usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:25, from /usr/include/boost/dynamic_bitset.hpp:15, from /<>/Code/DataStructs/ExplicitBitVect.h:16, from /<>/Code/DataStructs/FPBReader.cpp:15: /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from /usr/include/boost/core/swap.hpp:27, from /usr/include/boost/utility/swap.hpp:15, from /usr/include/boost/tuple/detail/tuple_basic.hpp:40, from /usr/include/boost/tuple/tuple.hpp:28, from /usr/include/boost/tuple/tuple_comparison.hpp:19, from /<>/Code/DataStructs/MultiFPBReader.cpp:11: /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = boost::tuples::tuple; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In member function ‘std::vector > RDKit::FPBReader::getTverskyNeighbors(const uint8_t*, double, double, double, bool) const’: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In member function ‘std::vector > RDKit::FPBReader::getTanimotoNeighbors(const uint8_t*, double, bool) const’: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from /usr/include/boost/core/swap.hpp:27, from /usr/include/boost/utility/swap.hpp:15, from /usr/include/boost/tuple/detail/tuple_basic.hpp:40, from /usr/include/boost/tuple/tuple.hpp:28, from /usr/include/boost/tuple/tuple_comparison.hpp:19, from /<>/Code/DataStructs/MultiFPBReader.cpp:11: /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:60, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/testDict.cpp:14: /usr/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, RDKit::RDAny>; _KeyOfValue = std::_Select1st, RDKit::RDAny> >; _Compare = std::less >; _Alloc = std::allocator, RDKit::RDAny> >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, RDKit::RDAny>, std::_Select1st, RDKit::RDAny> >, std::less >, std::allocator, RDKit::RDAny> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, RDKit::RDAny> >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/testDict.cpp:14: /usr/include/c++/9/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = RDKit::RDAny; _Compare = std::less >; _Alloc = std::allocator, RDKit::RDAny> >]’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, RDKit::RDAny>, std::_Select1st, RDKit::RDAny> >, std::less >, std::allocator, RDKit::RDAny> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, RDKit::RDAny> >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/testDict.cpp:14: /usr/include/c++/9/bits/stl_vector.h: In function ‘void testRDAny()’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Numerics /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Numerics /<>/obj-arm-linux-gnueabihf/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake --color= Scanning dependencies of target testMatrices make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 4%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/Numerics/testMatrices.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Ranking.h:21, from /<>/Code/DataStructs/MultiFPBReader.cpp:14: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {boost::tuples::tuple}; _Tp = boost::tuples::tuple; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {boost::tuples::tuple}; _Tp = boost::tuples::tuple; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Tp = boost::tuples::tuple; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 721 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Ranking.h:21, from /<>/Code/DataStructs/MultiFPBReader.cpp:14: /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::{anonymous}::generic_nbr_helper(std::vector >&, T, const RDKit::{anonymous}::sim_args&, unsigned int) [with T = void (*)(unsigned int, unsigned int, const RDKit::{anonymous}::sim_args*)]’: /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 1662 | _M_range_insert(__pos, __first, __last, | ^~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/9/algorithm:62, from /usr/include/boost/core/swap.hpp:27, from /usr/include/boost/utility/swap.hpp:15, from /usr/include/boost/tuple/detail/tuple_basic.hpp:40, from /usr/include/boost/tuple/tuple.hpp:28, from /usr/include/boost/tuple/tuple_comparison.hpp:19, from /<>/Code/DataStructs/MultiFPBReader.cpp:11: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 5%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2019.09.1 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.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 5%] Built target DataStructs make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Catalogs /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Catalogs /<>/obj-arm-linux-gnueabihf/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= Scanning dependencies of target Catalogs make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /<>/Code/Catalogs/Catalog.cpp [ 5%] Linking CXX executable testDict cd /<>/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 5%] Built target testDict make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Query /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Query /<>/obj-arm-linux-gnueabihf/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake --color= Scanning dependencies of target testQuery make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 6%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Query && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/Query/test.cpp [ 6%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Catalogs/CatalogParams.cpp [ 6%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Catalogs/CatalogEntry.cpp [ 6%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /<>/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2019.09.1 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 6%] Built target Catalogs make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/DataManip/MetricMatrixCalc /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc /<>/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= Scanning dependencies of target testMatCalc make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 7%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp [ 7%] Linking CXX executable testMatrices cd /<>/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 7%] Built target testMatrices make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/DataManip/MetricMatrixCalc/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap /<>/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= Scanning dependencies of target rdMetricMatrixCalc make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 8%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp [ 8%] Linking CXX executable testMatCalc cd /<>/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 8%] Built target testMatCalc make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/SimDivPickers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= Scanning dependencies of target SimDivPickers make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/DistPicker.cpp.o -c /<>/Code/SimDivPickers/DistPicker.cpp [ 9%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /<>/Code/SimDivPickers/MaxMinPicker.cpp In file included from /<>/Code/RDBoost/Wrap/RDBase.cpp:14: /<>/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)’: /<>/Code/RDBoost/python_streambuf.h:379:16: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 379 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 9%] Linking CXX executable testQuery cd /<>/obj-arm-linux-gnueabihf/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 /<>/Code/RDBoost/python_streambuf.h: In constructor ‘boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)’: /<>/Code/RDBoost/python_streambuf.h:186:56: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h:156:58: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 9%] Built target testQuery make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/ML/Cluster/Murtagh /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh /<>/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= Scanning dependencies of target Clustering make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 9%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ML/Cluster/Murtagh/Clustering.cpp [ 9%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/SimDivPickers/HierarchicalClusterPicker.cpp In file included from /<>/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:15: /<>/Code/RDBoost/PySequenceHolder.h: In function ‘double RDDataManip::EuclideanDistanceMetric(const T1&, const T2&, unsigned int) [with T1 = PySequenceHolder; T2 = PySequenceHolder]’: /<>/Code/RDBoost/PySequenceHolder.h:68:9: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ /<>/Code/RDBoost/PySequenceHolder.h:68:9: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/RDBoost/Wrap/RDBase.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/RDBoost/Wrap/RDBase.cpp:10: /usr/include/c++/9/bits/stl_vector.h: In function ‘void boost::python::container_utils::extend_container(Container&, boost::python::api::object) [with Container = std::vector]’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In static member function ‘static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 9%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /<>/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/RDBoost/Wrap/RDBase.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 184 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/RDBoost/Wrap/RDBase.cpp:10: /usr/include/c++/9/bits/stl_vector.h: In static member function ‘static void boost::python::indexing_suite::base_delete_item(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = double; Index = unsigned int; Key = double]’: /usr/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ In file included from /usr/include/c++/9/algorithm:62, from /usr/include/boost/function/detail/prologue.hpp:13, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /<>/Code/RDBoost/python.h:3, from /<>/Code/RDBoost/Wrap/RDBase.cpp:10: /usr/include/c++/9/bits/stl_algo.h: In function ‘_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]’: /usr/include/c++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 112 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h: In static member function ‘static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = double; Index = unsigned int; Key = double]’: /usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 162 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 162 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 9%] Built target rdMetricMatrixCalc make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/ML/InfoTheory /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/ML/InfoTheory /<>/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= Scanning dependencies of target InfoTheory make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 9%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ML/InfoTheory/InfoBitRanker.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/RDBoost/Wrap/RDBase.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 721 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/RDBoost/Wrap/RDBase.cpp:10: /usr/include/c++/9/bits/stl_vector.h: In static member function ‘static void boost::python::vector_indexing_suite::base_extend(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]’: /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 1662 | _M_range_insert(__pos, __first, __last, | ^~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_vector.h: In static member function ‘static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = double; Index = unsigned int]’: /usr/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/RDBoost/Wrap/RDBase.cpp:10: /usr/include/c++/9/bits/vector.tcc:161:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | _M_realloc_insert(begin() + (__position - cbegin()), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/RDBoost/Wrap/RDBase.cpp:10: /usr/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/RDBoost/Wrap/RDBase.cpp:10: /usr/include/c++/9/bits/vector.tcc:161:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | _M_realloc_insert(begin() + (__position - cbegin()), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/RDBoost/Wrap/RDBase.cpp:10: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 1662 | _M_range_insert(__pos, __first, __last, | ^~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 1662 | _M_range_insert(__pos, __first, __last, | ^~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 [ 9%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2019.09.1 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2019.09.1 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 9%] Built target SimDivPickers make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Geometry /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Geometry /<>/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= Scanning dependencies of target RDGeometryLib make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Geometry/point.cpp [ 9%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /<>/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 9%] Built target Clustering make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/DataStructs /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/DataStructs /<>/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= Scanning dependencies of target testFPB make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 9%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/DataStructs/testFPB.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/ML/InfoTheory/InfoBitRanker.h:15, from /<>/Code/ML/InfoTheory/InfoBitRanker.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/ML/InfoTheory/InfoBitRanker.h:15, from /<>/Code/ML/InfoTheory/InfoBitRanker.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In member function ‘double* RDInfoTheory::InfoBitRanker::getTopN(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 9%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /<>/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2019.09.1 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2019.09.1 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 9%] Built target InfoTheory make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/DataStructs /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/DataStructs /<>/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= Scanning dependencies of target testDataStructs make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 9%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/DataStructs/testDatastructs.cpp [ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Geometry/Transform2D.cpp /<>/Code/DataStructs/testDatastructs.cpp: In function ‘void test5DiscreteVectOps2()’: /<>/Code/DataStructs/testDatastructs.cpp:477:19: warning: implicitly-declared ‘RDKit::DiscreteValueVect& RDKit::DiscreteValueVect::operator=(const RDKit::DiscreteValueVect&)’ is deprecated [-Wdeprecated-copy] 477 | vect5 = vect1 - vect2; | ^~~~~ In file included from /<>/Code/DataStructs/testDatastructs.cpp:22: /<>/Code/DataStructs/DiscreteValueVect.h:50:3: note: because ‘RDKit::DiscreteValueVect’ has user-provided ‘RDKit::DiscreteValueVect::DiscreteValueVect(const RDKit::DiscreteValueVect&)’ 50 | DiscreteValueVect(const DiscreteValueVect &other); | ^~~~~~~~~~~~~~~~~ /<>/Code/DataStructs/testDatastructs.cpp:479:19: warning: implicitly-declared ‘RDKit::DiscreteValueVect& RDKit::DiscreteValueVect::operator=(const RDKit::DiscreteValueVect&)’ is deprecated [-Wdeprecated-copy] 479 | vect5 = vect2 - vect1; | ^~~~~ In file included from /<>/Code/DataStructs/testDatastructs.cpp:22: /<>/Code/DataStructs/DiscreteValueVect.h:50:3: note: because ‘RDKit::DiscreteValueVect’ has user-provided ‘RDKit::DiscreteValueVect::DiscreteValueVect(const RDKit::DiscreteValueVect&)’ 50 | DiscreteValueVect(const DiscreteValueVect &other); | ^~~~~~~~~~~~~~~~~ /<>/Code/DataStructs/testDatastructs.cpp: In function ‘void test6SparseIntVect()’: /<>/Code/DataStructs/testDatastructs.cpp:627:17: warning: implicitly-declared ‘RDKit::SparseIntVect& RDKit::SparseIntVect::operator=(const RDKit::SparseIntVect&)’ is deprecated [-Wdeprecated-copy] 627 | iV3 = iV1 & iV2; | ^~~ In file included from /<>/Code/DataStructs/testDatastructs.cpp:26: /<>/Code/DataStructs/SparseIntVect.h:38:3: note: because ‘RDKit::SparseIntVect’ has user-provided ‘RDKit::SparseIntVect::SparseIntVect(const RDKit::SparseIntVect&) [with IndexType = int]’ 38 | SparseIntVect(const SparseIntVect &other) { | ^~~~~~~~~~~~~ /<>/Code/DataStructs/testDatastructs.cpp:725:17: warning: implicitly-declared ‘RDKit::SparseIntVect& RDKit::SparseIntVect::operator=(const RDKit::SparseIntVect&)’ is deprecated [-Wdeprecated-copy] 725 | iV3 = iV1 | iV2; | ^~~ In file included from /<>/Code/DataStructs/testDatastructs.cpp:26: /<>/Code/DataStructs/SparseIntVect.h:38:3: note: because ‘RDKit::SparseIntVect’ has user-provided ‘RDKit::SparseIntVect::SparseIntVect(const RDKit::SparseIntVect&) [with IndexType = int]’ 38 | SparseIntVect(const SparseIntVect &other) { | ^~~~~~~~~~~~~ /<>/Code/DataStructs/testDatastructs.cpp:808:17: warning: implicitly-declared ‘RDKit::SparseIntVect& RDKit::SparseIntVect::operator=(const RDKit::SparseIntVect&)’ is deprecated [-Wdeprecated-copy] 808 | iV3 = iV1 + iV2; | ^~~ In file included from /<>/Code/DataStructs/testDatastructs.cpp:26: /<>/Code/DataStructs/SparseIntVect.h:38:3: note: because ‘RDKit::SparseIntVect’ has user-provided ‘RDKit::SparseIntVect::SparseIntVect(const RDKit::SparseIntVect&) [with IndexType = int]’ 38 | SparseIntVect(const SparseIntVect &other) { | ^~~~~~~~~~~~~ /<>/Code/DataStructs/testDatastructs.cpp:864:17: warning: implicitly-declared ‘RDKit::SparseIntVect& RDKit::SparseIntVect::operator=(const RDKit::SparseIntVect&)’ is deprecated [-Wdeprecated-copy] 864 | iV3 = iV1 - iV2; | ^~~ In file included from /<>/Code/DataStructs/testDatastructs.cpp:26: /<>/Code/DataStructs/SparseIntVect.h:38:3: note: because ‘RDKit::SparseIntVect’ has user-provided ‘RDKit::SparseIntVect::SparseIntVect(const RDKit::SparseIntVect&) [with IndexType = int]’ 38 | SparseIntVect(const SparseIntVect &other) { | ^~~~~~~~~~~~~ [ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Geometry/Transform3D.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/DataStructs/BitVect.h:14, from /<>/Code/DataStructs/BitVects.h:19, from /<>/Code/DataStructs/testDatastructs.cpp:17: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 11%] Linking CXX executable testFPB cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 11%] Built target testFPB make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/DataStructs /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/DataStructs /<>/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= Scanning dependencies of target testMultiFPB make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 11%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/DataStructs/testMultiFPB.cpp [ 11%] Linking CXX shared module ../../../rdkit/rdBase.so cd /<>/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 11%] Built target rdBase make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/DataStructs/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap /<>/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= Scanning dependencies of target cDataStructs make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/Wrap/DataStructs.cpp [ 11%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Geometry/UniformGrid3D.cpp /usr/include/c++/9/bits/vector.tcc: In function ‘void test16BitVectProps()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /<>/Code/Geometry/UniformGrid3D.cpp: In member function ‘RDGeom::UniformGrid3D& RDGeom::UniformGrid3D::operator=(const RDGeom::UniformGrid3D&)’: /<>/Code/Geometry/UniformGrid3D.cpp:39:11: warning: control reaches end of non-void function [-Wreturn-type] 39 | initGrid(other.d_numX * other.d_spacing, other.d_numY * other.d_spacing, | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | other.d_numZ * other.d_spacing, other.d_spacing, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 | other.dp_storage->getValueType(), other.d_offSet, data); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 11%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Geometry/GridUtils.cpp [ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/Wrap/DiscreteValueVect.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Geometry/GridUtils.h:14, from /<>/Code/Geometry/GridUtils.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Geometry/GridUtils.h:14, from /<>/Code/Geometry/GridUtils.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In function ‘std::vector RDGeom::findGridTerminalPoints(const RDGeom::UniformGrid3D&, double, double)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 11%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /<>/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 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.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 11%] Built target RDGeometryLib make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/SimDivPickers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= Scanning dependencies of target pickersTestsCatch make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 11%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/SimDivPickers/catch_tests.cpp [ 11%] Linking CXX executable testMultiFPB cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 11%] Built target testMultiFPB make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/SimDivPickers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= Scanning dependencies of target testSimDivPickers make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 12%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/SimDivPickers/testPickers.cpp [ 12%] Linking CXX executable testDataStructs cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 12%] Built target testDataStructs make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/SimDivPickers/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= Scanning dependencies of target rdSimDivPickers make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/SimDivPickers/Wrap/MaxMinPicker.cpp [ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/Wrap/SparseIntVect.cpp [ 12%] Linking CXX executable testSimDivPickers cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread ../../lib/libRDKithc.so.1.2019.09.1 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 12%] Built target testSimDivPickers make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/ML/InfoTheory/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap /<>/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= Scanning dependencies of target rdInfoTheory make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 12%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp In file included from /<>/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:19: /<>/Code/SimDivPickers/Wrap/PickerHelpers.h: In member function ‘RDKit::INT_VECT RDPickers::MaxMinPicker::lazyPick(T&, unsigned int, unsigned int, const INT_VECT&, int, double&) const [with T = pyobjFunctor]’: /<>/Code/SimDivPickers/Wrap/PickerHelpers.h:53:48: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 53 | return python::extract(dp_obj(i, j)); | ^ /<>/Code/SimDivPickers/Wrap/PickerHelpers.h:53:48: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 53 | return python::extract(dp_obj(i, j)); | ^ [ 12%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp [ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/SimDivPickers/Wrap/LeaderPicker.cpp In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/SimDivPickers/catch_tests.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/SimDivPickers/catch_tests.cpp:13: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 13%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp In file included from /<>/Code/SimDivPickers/Wrap/LeaderPicker.cpp:19: /<>/Code/SimDivPickers/Wrap/PickerHelpers.h: In member function ‘RDKit::INT_VECT RDPickers::LeaderPicker::lazyPick(T&, unsigned int, unsigned int, const INT_VECT&, double, int) const [with T = pyobjFunctor]’: /<>/Code/SimDivPickers/Wrap/PickerHelpers.h:53:48: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 53 | return python::extract(dp_obj(i, j)); | ^ /<>/Code/SimDivPickers/Wrap/PickerHelpers.h:53:48: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 53 | return python::extract(dp_obj(i, j)); | ^ In file included from /<>/Code/DataStructs/Wrap/SparseIntVect.cpp:18: /<>/Code/RDBoost/PySequenceHolder.h: In function ‘void {anonymous}::pyUpdateFromSequence(RDKit::SparseIntVect&, boost::python::api::object&) [with IndexType = long long int]’: /<>/Code/RDBoost/PySequenceHolder.h:68:9: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ [ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp /<>/Code/RDBoost/PySequenceHolder.h: In function ‘void {anonymous}::pyUpdateFromSequence(RDKit::SparseIntVect&, boost::python::api::object&) [with IndexType = long long unsigned int]’: /<>/Code/RDBoost/PySequenceHolder.h:68:9: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ [ 13%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so cd /<>/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -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.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 13%] Built target rdInfoTheory make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/ML/Data /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/ML/Data /<>/obj-arm-linux-gnueabihf/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= Scanning dependencies of target cQuantize make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 13%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ML/Data && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ML/Data/cQuantize.cpp [ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp [ 13%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so cd /<>/obj-arm-linux-gnueabihf/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2019.09.1 ../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 13%] Built target cQuantize make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/ChemicalFeatures /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target ChemicalFeatures make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 13%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ChemicalFeatures/FreeChemicalFeature.cpp [ 13%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2019.09.1 ../../../lib/libRDKithc.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 13%] Built target rdSimDivPickers make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= Scanning dependencies of target GraphMol make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Atom.cpp [ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/Wrap/wrap_SparseBV.cpp [ 14%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2019.09.1 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2019.09.1 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 14%] Built target ChemicalFeatures make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Numerics/Alignment /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /<>/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= Scanning dependencies of target Alignment make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 14%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Numerics/Alignment/AlignPoints.cpp [ 14%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2019.09.1 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 14%] Built target Alignment make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Geometry /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Geometry /<>/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake --color= Scanning dependencies of target geometryTestsCatch make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 14%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /<>/Code/Geometry/catch_tests.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/Atom.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/QueryAtom.cpp [ 15%] Linking CXX executable pickersTestsCatch cd /<>/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../../lib/libRDKitSimDivPickers.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 ../../lib/libRDKithc.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 15%] Built target pickersTestsCatch make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Geometry /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Geometry /<>/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= Scanning dependencies of target testGrid make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 15%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/Geometry/testGrid.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/QueryBond.cpp [ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/Wrap/wrap_BitOps.cpp [ 16%] Linking CXX executable testGrid cd /<>/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 16%] Built target testGrid make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Geometry /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Geometry /<>/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target testTransforms make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 16%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/Geometry/testTransforms.cpp In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/Geometry/catch_tests.cpp:3: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/Geometry/catch_tests.cpp:3: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Bond.cpp [ 17%] Linking CXX executable testTransforms cd /<>/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 17%] Built target testTransforms make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Geometry/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Geometry/Wrap /<>/obj-arm-linux-gnueabihf/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= Scanning dependencies of target rdGeometry make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Geometry/Wrap/Point.cpp [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolOps.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/MolOps.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/MolOps.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/MolOps.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/MolOps.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In function ‘std::map > RDKit::MolOps::getMolFragsWithQuery(const RDKit::ROMol&, T (*)(const RDKit::ROMol&, const RDKit::Atom*), bool, const std::vector*, bool) [with T = std::__cxx11::basic_string]’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘std::map > RDKit::MolOps::getMolFragsWithQuery(const RDKit::ROMol&, T (*)(const RDKit::ROMol&, const RDKit::Atom*), bool, const std::vector*, bool) [with T = int]’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘std::map > RDKit::MolOps::getMolFragsWithQuery(const RDKit::ROMol&, T (*)(const RDKit::ROMol&, const RDKit::Atom*), bool, const std::vector*, bool) [with T = unsigned int]’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/MolOps.cpp:11: /usr/include/c++/9/bits/vector.tcc: In function ‘std::vector > RDKit::MolOps::getMolFrags(const RDKit::ROMol&, bool, RDKit::INT_VECT*, RDKit::VECT_INT_VECT*, bool)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/MolOps.cpp:11: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/Wrap/wrap_FPB.cpp [ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Geometry/Wrap/UniformGrid3D.cpp [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FindRings.cpp /<>/Code/GraphMol/FindRings.cpp: In function ‘int RDKit::MolOps::symmetrizeSSSR(RDKit::ROMol&, RDKit::VECT_INT_VECT&)’: /<>/Code/GraphMol/FindRings.cpp:1103:16: warning: variable ‘nsssr’ set but not used [-Wunused-but-set-variable] 1103 | unsigned int nsssr; | ^~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/FindRings.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 17%] Linking CXX executable geometryTestsCatch cd /<>/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 17%] Built target geometryTestsCatch make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Numerics /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Numerics /<>/obj-arm-linux-gnueabihf/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake --color= Scanning dependencies of target testConrec make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 17%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/Numerics/testConrec.cpp [ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DataStructs/Wrap/wrap_Utils.cpp [ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Geometry/Wrap/rdGeometry.cpp [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ROMol.cpp [ 18%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /<>/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -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.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 18%] Built target rdGeometry make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Numerics/Alignment /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /<>/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= Scanning dependencies of target testAlignment make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 18%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/Numerics/Alignment/testAlignment.cpp [ 18%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /<>/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -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.1.2019.09.1 ../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 18%] Built target cDataStructs make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Numerics/Alignment/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap /<>/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= Scanning dependencies of target rdAlignment make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 18%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Numerics/Alignment/Wrap/rdAlignment.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/ROMol.cpp:17: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, T&) [with T = std::vector >]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 18%] Linking CXX executable testAlignment cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 18%] Built target testAlignment make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/ChemicalFeatures /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target testChemicalFeatures make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 18%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/ROMol.cpp:17: /usr/include/c++/9/bits/stl_vector.h: In member function ‘unsigned int RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ cd /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/ChemicalFeatures/testChemicalFeatures.cpp In file included from /<>/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:16: /<>/Code/RDBoost/PySequenceHolder.h: In member function ‘T PySequenceHolder::operator[](unsigned int) const [with T = double]’: /<>/Code/RDBoost/PySequenceHolder.h:68:9: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/RWMol.cpp [ 20%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 20%] Built target rdAlignment [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/PeriodicTable.cpp [ 21%] Linking CXX executable testChemicalFeatures cd /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures ../../lib/libRDKitChemicalFeatures.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 21%] Built target testChemicalFeatures [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/atomic_data.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/PeriodicTable.h:15, from /<>/Code/GraphMol/PeriodicTable.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDKit::atomicData&}; _Tp = RDKit::atomicData; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/GraphMol/PeriodicTable.h:15, from /<>/Code/GraphMol/PeriodicTable.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::PeriodicTable::PeriodicTable()’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/Numerics/testConrec.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/Numerics/testConrec.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/QueryOps.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolPickler.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/RWMol.h:21, from /<>/Code/GraphMol/RWMol.cpp:16: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/RWMol.h:21, from /<>/Code/GraphMol/RWMol.cpp:16: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/RWMol.h:21, from /<>/Code/GraphMol/RWMol.cpp:16: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/RWMol.h:21, from /<>/Code/GraphMol/RWMol.cpp:16: /usr/include/c++/9/bits/stl_vector.h: In member function ‘void RDKit::RWMol::insertMol(const RDKit::ROMol&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In member function ‘unsigned int RDKit::RWMol::addAtom(bool)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Canon.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/AtomIterators.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolPickler.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolPickler.cpp:10: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolPickler.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Canon.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolPickler.cpp:10: /usr/include/c++/9/bits/stl_vector.h: In static member function ‘static void RDKit::MolPickler::_addAtomFromPickleV1(std::istream&, RDKit::ROMol*)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/BondIterators.cpp [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Aromaticity.cpp [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Kekulize.cpp [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolDiscriminators.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Aromaticity.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ConjugHybrid.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/MolOps.h:15, from /<>/Code/GraphMol/MolDiscriminators.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/AddHs.cpp [ 22%] Linking CXX executable testConrec cd /<>/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConrec.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testConrec.dir/testConrec.cpp.o -o testConrec ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 22%] Built target testConrec [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Matrices.cpp [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Chirality.cpp [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/RingInfo.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/Matrices.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Conformer.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/AddHs.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/AddHs.cpp:10: /usr/include/c++/9/bits/stl_vector.h: In member function ‘void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/AddHs.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Renumber.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Chirality.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/AddHs.cpp:10: /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::{anonymous}::setHydrogenCoords(RDKit::ROMol*, unsigned int, unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/AdjustQuery.cpp [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Resonance.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/Renumber.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/Renumber.cpp:10: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/Renumber.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/Renumber.cpp:10: /usr/include/c++/9/bits/stl_vector.h: In function ‘RDKit::ROMol* RDKit::MolOps::renumberAtoms(const RDKit::ROMol&, const std::vector&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/StereoGroup.cpp [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/new_canon.cpp [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SubstanceGroup.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Resonance.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Geometry/point.h:16, from /<>/Code/GraphMol/SubstanceGroup.h:22, from /<>/Code/GraphMol/SubstanceGroup.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::array&}; _Tp = std::array; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Geometry/point.h:16, from /<>/Code/GraphMol/SubstanceGroup.h:22, from /<>/Code/GraphMol/SubstanceGroup.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In member function ‘void RDKit::SubstanceGroup::addBracket(const Bracket&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Geometry/point.h:16, from /<>/Code/GraphMol/SubstanceGroup.h:22, from /<>/Code/GraphMol/SubstanceGroup.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::SubstanceGroup::CState}; _Tp = RDKit::SubstanceGroup::CState; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In function ‘void RDKit::ResonanceUtils::fixExplicitImplicitHs(RDKit::ROMol&)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::SubstanceGroup::addCState(unsigned int, const RDGeom::Point3D&)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In constructor ‘RDKit::SubstanceGroup::SubstanceGroup(RDKit::ROMol*, const string&)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 24%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2019.09.1 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 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 24%] Built target GraphMol make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Trajectory /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/SmilesParse /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Substruct /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolTransforms /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target SmilesParse make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build Scanning dependencies of target Trajectory Scanning dependencies of target SubstructMatch make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' Scanning dependencies of target MolTransforms [ 25%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /<>/Code/GraphMol/Trajectory/Trajectory.cpp make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build [ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SmilesParse/SmilesParse.cpp [ 25%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Substruct/SubstructMatch.cpp make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 26%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolTransforms/MolTransforms.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/Trajectory/Trajectory.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/Trajectory/Trajectory.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/Trajectory/Trajectory.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:130:5: note: parameter passing for argument of type ‘std::vector::const_iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 130 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:161:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | _M_realloc_insert(begin() + (__position - cbegin()), __x); | ^~~~~~~~~~~~~~~~~ /<>/Code/GraphMol/Trajectory/Trajectory.cpp: In member function ‘unsigned int RDKit::Trajectory::insertSnapshot(unsigned int, RDKit::Snapshot)’: /<>/Code/GraphMol/Trajectory/Trajectory.cpp:73:74: note: parameter passing for argument of type ‘std::vector::const_iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 73 | return (d_snapshotVect->insert(d_snapshotVect->begin() + snapshotNum, s) - | ^ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/Trajectory/Trajectory.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘unsigned int RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/RWMol.h:21, from /<>/Code/GraphMol/SmilesParse/SmilesParse.h:14, from /<>/Code/GraphMol/SmilesParse/SmilesParse.cpp:26: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, T&) [with T = std::__cxx11::basic_string]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 26%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2019.09.1 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 26%] Built target Trajectory make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Subgraphs /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= Scanning dependencies of target Subgraphs make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 26%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/<>/External/boost-numeric-bindings -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Subgraphs/Subgraphs.cpp [ 26%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 26%] Built target MolTransforms make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/PartialCharges /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= Scanning dependencies of target PartialCharges make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 26%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/PartialCharges/GasteigerCharges.cpp [ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SmilesParse/SmilesParseOps.cpp [ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Substruct/SubstructUtils.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/PartialCharges/GasteigerCharges.h:14, from /<>/Code/GraphMol/PartialCharges/GasteigerCharges.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/GraphMol/PartialCharges/GasteigerCharges.h:14, from /<>/Code/GraphMol/PartialCharges/GasteigerCharges.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::computeGasteigerCharges(const RDKit::ROMol&, std::vector&, int, bool)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 27%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/PartialCharges/GasteigerParams.cpp [ 27%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/<>/External/boost-numeric-bindings -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Subgraphs/SubgraphUtils.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/SmilesParse/SmilesParseOps.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 27%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 27%] Built target SubstructMatch make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolTransforms/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolTransforms make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 28%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp [ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SmilesParse/SmilesWrite.cpp [ 28%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 28%] Built target PartialCharges make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ShapeHelpers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target ShapeHelpers make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 28%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /<>/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/Subgraphs/Subgraphs.h:32, from /<>/Code/GraphMol/Subgraphs/SubgraphUtils.h:14, from /<>/Code/GraphMol/Subgraphs/SubgraphUtils.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/GraphMol/Subgraphs/Subgraphs.h:32, from /<>/Code/GraphMol/Subgraphs/SubgraphUtils.h:14, from /<>/Code/GraphMol/Subgraphs/SubgraphUtils.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘RDKit::ROMol* RDKit::Subgraphs::pathToSubmol(const RDKit::ROMol&, const PATH_TYPE&, bool, RDKit::INT_MAP_INT&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 29%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 29%] Built target Subgraphs make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolCatalog /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target MolCatalog make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 29%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp [ 29%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/SmilesParse/SmilesWrite.h:15, from /<>/Code/GraphMol/SmilesParse/SmilesWrite.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/ShapeHelpers/ShapeUtils.h:14, from /<>/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/Code/GraphMol/ShapeHelpers/ShapeUtils.h:14, from /<>/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In function ‘std::vector RDKit::MolShapes::getConfDimensions(const RDKit::Conformer&, double, const RDGeom::Point3D*, bool)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 29%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2019.09.1 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2019.09.1 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 29%] Built target ShapeHelpers make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolInterchange /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --color= Scanning dependencies of target MolInterchange make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 29%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/rapidjson -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolInterchange/Parser.cpp [ 29%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread [ 29%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolCatalog/MolCatalogParams.cpp make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 29%] Built target rdMolTransforms make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/SLNParse /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= Scanning dependencies of target SLNParse make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 29%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SLNParse/SLNParse.cpp [ 30%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SmilesParse/SmartsWrite.cpp [ 31%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2019.09.1 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2019.09.1 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 31%] Built target MolCatalog make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= Scanning dependencies of target rdqueries make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 31%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/rdqueries.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolInterchange/Parser.cpp:16: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolInterchange/Parser.cpp:16: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolInterchange/Parser.cpp:16: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolInterchange/Parser.cpp:16: /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::MolInterchange::{anonymous}::readConformer(RDKit::Conformer*, const Value&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/SmilesParse/SmartsWrite.h:15, from /<>/Code/GraphMol/SmilesParse/SmartsWrite.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘std::string RDKit::{anonymous}::getAtomSmartsSimple(const RDKit::QueryAtom*, const ATOM_EQUALS_QUERY*, bool&)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/SLNParse/SLNParse.cpp:35: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘void RDKit::SLNParse::finalizeQueryMol(RDKit::ROMol*, bool)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘std::string RDKit::SmartsWrite::GetAtomSmarts(const RDKit::QueryAtom*)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 31%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/Queries.cpp /usr/include/c++/9/bits/vector.tcc: In function ‘std::string RDKit::{anonymous}::molToSmarts(const RDKit::ROMol&, bool, std::vector&&, const boost::dynamic_bitset<>*)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 31%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/rapidjson -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolInterchange/Writer.cpp [ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SmilesParse/CXSmilesOps.cpp [ 31%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SLNParse/SLNAttribs.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:13: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/SLNParse/SLNAttribs.h:39, from /<>/Code/GraphMol/SLNParse/SLNAttribs.cpp:37: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 31%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2019.09.1 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2019.09.1 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 31%] Built target MolInterchange make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= Scanning dependencies of target rdtrajectory make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 31%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/Trajectory.cpp [ 32%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SLNParse/sln.tab.cpp In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:13: /usr/include/c++/9/bits/stl_vector.h: In function ‘bool SmilesParseOps::parser::parse_coords(Iterator&, Iterator, RDKit::RWMol&) [with Iterator = __gnu_cxx::__normal_iterator >]’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 32%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SmilesParse/smarts.tab.cpp [ 32%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 32%] Built target rdqueries make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/ChemicalFeatures/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target rdChemicalFeatures make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 32%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp In file included from /usr/include/c++/9/vector:72, from sln.yy:41: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from smarts.yy:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 32%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/rdTrajectory.cpp [ 32%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SLNParse/lex.yysln.cpp [ 33%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp [ 33%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SmilesParse/smiles.tab.cpp [ 34%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -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.1.2019.09.1 ../../../lib/libRDKitRDBoost.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 34%] Built target rdtrajectory make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Numerics/Optimizer /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer /<>/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= Scanning dependencies of target Optimizer make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 34%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Numerics/Optimizer/BFGSOpt.cpp [ 34%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2019.09.1 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.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2019.09.1 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 34%] Built target SLNParse make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/PartialCharges/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= Scanning dependencies of target rdPartialCharges make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 34%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp [ 34%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/Numerics/Optimizer/LinearSearch.cpp In file included from /usr/include/c++/9/vector:72, from smiles.yy:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 34%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2019.09.1 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 34%] 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 '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ShapeHelpers/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target rdShapeHelpers make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 34%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp [ 34%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so cd /<>/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../../lib/libRDKitChemicalFeatures.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread [ 34%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SmilesParse/lex.yysmarts.cpp make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 34%] Built target rdChemicalFeatures make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolInterchange/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolInterchange make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 34%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/rapidjson -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp [ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 34%] Built target rdPartialCharges make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/ForceField /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/ForceField /<>/obj-arm-linux-gnueabihf/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= Scanning dependencies of target ForceField make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /<>/Code/ForceField/ForceField.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/ForceField/ForceField.h:14, from /<>/Code/ForceField/ForceField.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 [ 34%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SmilesParse/lex.yysmiles.cpp In file included from /usr/include/c++/9/vector:67, from /<>/Code/ForceField/ForceField.h:14, from /<>/Code/ForceField/ForceField.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In member function ‘double ForceFields::ForceField::calcEnergy(std::vector*) const’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/Conformer.h:14, from /<>/Code/GraphMol/ROMol.h:36, from /<>/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:13: /<>/Code/Geometry/point.h: In function ‘boost::python::tuple RDKit::getUnionOfTwoBox(boost::python::tuple, boost::python::tuple)’: /<>/Code/Geometry/point.h:56:31: warning: ‘*((void*)(&)+16).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /<>/Code/Geometry/point.h:56:43: warning: ‘*((void*)(&)+16).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /<>/Code/Geometry/point.h:56:55: warning: ‘*((void*)(&)+16).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /<>/Code/Geometry/point.h:56:31: warning: ‘*((void*)(&)+16).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /<>/Code/Geometry/point.h:56:43: warning: ‘*((void*)(&)+16).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /<>/Code/Geometry/point.h:56:55: warning: ‘*((void*)(&)+16).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /<>/Code/Geometry/point.h:56:31: warning: ‘*((void*)(&)+16).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /<>/Code/Geometry/point.h:56:43: warning: ‘*((void*)(&)+16).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /<>/Code/Geometry/point.h:56:55: warning: ‘*((void*)(&)+16).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /<>/Code/Geometry/point.h:56:31: warning: ‘*((void*)(&)+16).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /<>/Code/Geometry/point.h:56:43: warning: ‘*((void*)(&)+16).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /<>/Code/Geometry/point.h:56:55: warning: ‘*((void*)(&)+16).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /usr/include/c++/9/bits/stl_vector.h: In function ‘int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = ForceFieldsHelper::calcEnergy; GradientFunctor = ForceFieldsHelper::calcGradient]’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 34%] Built target rdMolInterchange make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/Numerics/Optimizer /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer /<>/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= Scanning dependencies of target testOptimizer make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 35%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/Numerics/Optimizer/testOptimizer.cpp [ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ForceField/UFF/AngleBend.cpp [ 35%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 35%] Built target rdShapeHelpers [ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /<>/Code/ForceField/UFF/BondStretch.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Geometry/point.h:16, from /<>/Code/GraphMol/Trajectory/Snapshot.h:14, from /<>/Code/Numerics/Optimizer/BFGSOpt.h:13, from /<>/Code/Numerics/Optimizer/testOptimizer.cpp:16: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Geometry/point.h:16, from /<>/Code/GraphMol/Trajectory/Snapshot.h:14, from /<>/Code/Numerics/Optimizer/BFGSOpt.h:13, from /<>/Code/Numerics/Optimizer/testOptimizer.cpp:16: /usr/include/c++/9/bits/stl_vector.h: In function ‘int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from smiles.ll:25: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ForceField/UFF/Nonbonded.cpp [ 35%] Linking CXX executable testOptimizer cd /<>/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 35%] Built target testOptimizer [ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ForceField/UFF/Inversion.cpp [ 36%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 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.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 36%] Built target SmilesParse make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolSGroupCatch make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 37%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/catch_sgroups.cpp [ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ForceField/UFF/TorsionAngle.cpp [ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /<>/Code/ForceField/UFF/DistanceConstraint.cpp [ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c /<>/Code/ForceField/UFF/AngleConstraint.cpp [ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ForceField/UFF/TorsionConstraint.cpp [ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ForceField/UFF/PositionConstraint.cpp [ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ForceField/UFF/Params.cpp [ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /<>/Code/ForceField/MMFF/AngleBend.cpp [ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /<>/Code/ForceField/MMFF/BondStretch.cpp make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolqueryTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 38%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/querytest.cpp [ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/StretchBend.cpp.o -c /<>/Code/ForceField/MMFF/StretchBend.cpp [ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ForceField/MMFF/OopBend.cpp [ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /<>/Code/ForceField/MMFF/TorsionAngle.cpp [ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ForceField/MMFF/Nonbonded.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/querytest.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 39%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/DistanceConstraint.cpp.o -c /<>/Code/ForceField/MMFF/DistanceConstraint.cpp In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/catch_sgroups.cpp:14: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/catch_sgroups.cpp:14: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolcpTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 39%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/cptest.cpp [ 39%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ForceField/MMFF/AngleConstraint.cpp [ 39%] Linking CXX executable graphmolqueryTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 39%] Built target graphmolqueryTest make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolMemTest1 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 39%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /<>/Code/GraphMol/memtest1.cpp In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/catch_sgroups.cpp:14: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 39%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ForceField/MMFF/TorsionConstraint.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/cptest.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/cptest.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 40%] Linking CXX executable graphmolcpTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 40%] Built target graphmolcpTest make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= Scanning dependencies of target test-valgrind In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/memtest1.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 40%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/test-valgrind.cpp [ 40%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /<>/Code/ForceField/MMFF/PositionConstraint.cpp /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 40%] Linking CXX executable graphmolMemTest1 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 40%] Built target graphmolMemTest1 make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolIterTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 41%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/itertest.cpp [ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ForceField/MMFF/Params.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/ForceField/MMFF/Params.h:20, from /<>/Code/ForceField/MMFF/Params.cpp:17: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFPBCI&}; _Tp = ForceFields::MMFF::MMFFPBCI; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFChg&}; _Tp = ForceFields::MMFF::MMFFChg; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFBond&}; _Tp = ForceFields::MMFF::MMFFBond; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFHerschbachLaurie&}; _Tp = ForceFields::MMFF::MMFFHerschbachLaurie; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 [ 41%] Linking CXX executable test-valgrind cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFCovRadPauEle&}; _Tp = ForceFields::MMFF::MMFFCovRadPauEle; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -o test-valgrind ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFAngle&}; _Tp = ForceFields::MMFF::MMFFAngle; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFStbn&}; _Tp = ForceFields::MMFF::MMFFStbn; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFOop&}; _Tp = ForceFields::MMFF::MMFFOop; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFTor&}; _Tp = ForceFields::MMFF::MMFFTor; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFVdW&}; _Tp = ForceFields::MMFF::MMFFVdW; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 41%] Built target test-valgrind make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ChemTransforms /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target ChemTransforms make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 41%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ChemTransforms/ChemTransforms.cpp In file included from /usr/include/c++/9/vector:67, from /<>/Code/ForceField/MMFF/Params.h:20, from /<>/Code/ForceField/MMFF/Params.cpp:17: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘ForceFields::MMFF::MMFFHerschbachLaurieCollection::MMFFHerschbachLaurieCollection(std::string)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘ForceFields::MMFF::MMFFBndkCollection::MMFFBndkCollection(std::string)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘ForceFields::MMFF::MMFFBondCollection::MMFFBondCollection(std::string)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘ForceFields::MMFF::MMFFChgCollection::MMFFChgCollection(std::string)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘ForceFields::MMFF::MMFFCovRadPauEleCollection::MMFFCovRadPauEleCollection(std::string)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘ForceFields::MMFF::MMFFOopCollection::MMFFOopCollection(bool, std::string)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘ForceFields::MMFF::MMFFStbnCollection::MMFFStbnCollection(std::string)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘ForceFields::MMFF::MMFFAngleCollection::MMFFAngleCollection(std::string)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘ForceFields::MMFF::MMFFPBCICollection::MMFFPBCICollection(std::string)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘ForceFields::MMFF::MMFFTorCollection::MMFFTorCollection(bool, std::string)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘ForceFields::MMFF::MMFFVdWCollection::MMFFVdWCollection(std::string)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 41%] Linking CXX executable graphmolIterTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 41%] Built target graphmolIterTest make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/SmilesParse /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= Scanning dependencies of target smaTest1 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 41%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/SmilesParse/smatest.cpp [ 41%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2019.09.1 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.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 41%] Built target ForceField make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/SmilesParse /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= Scanning dependencies of target smiTest2 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 41%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/SmilesParse/test2.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:10: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::{anonymous}::updateSubMolConfs(const RDKit::ROMol&, RDKit::RWMol&, boost::dynamic_bitset<>&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘RDKit::ROMol* RDKit::combineMols(const RDKit::ROMol&, const RDKit::ROMol&, RDGeom::Point3D)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 41%] Linking CXX executable smiTest2 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 41%] Built target smiTest2 make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FilterCatalog /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target FilterCatalog make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 41%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/Filters.cpp.o -c /<>/Code/GraphMol/FilterCatalog/Filters.cpp /usr/include/c++/9/bits/stl_vector.h: In function ‘RDKit::ROMol* RDKit::replaceCore(const RDKit::ROMol&, const RDKit::ROMol&, const MatchVectType&, bool, bool, bool)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 41%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /<>/Code/GraphMol/ChemTransforms/MolFragmenter.cpp [ 41%] Linking CXX executable graphmolSGroupCatch cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 41%] Built target graphmolSGroupCatch make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Fingerprints /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= Scanning dependencies of target Fingerprints make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /<>/Code/GraphMol/Fingerprints/Fingerprints.cpp [ 41%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/FilterCatalog.cpp.o -c /<>/Code/GraphMol/FilterCatalog/FilterCatalog.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/ChemTransforms/MolFragmenter.h:15, from /<>/Code/GraphMol/ChemTransforms/MolFragmenter.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /<>/Code/RDGeneral/RDLog.h:17, from /<>/Code/RDGeneral/Invariant.h:22, from /<>/Code/GraphMol/RDKitBase.h:21, from /<>/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: /usr/include/c++/9/bits/stl_algo.h: In function ‘_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]’: /usr/include/c++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 112 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/set:60, from /<>/Code/Query/SetQuery.h:13, from /<>/Code/Query/QueryObjects.h:29, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: /usr/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator > > >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/ChemTransforms/MolFragmenter.h:15, from /<>/Code/GraphMol/ChemTransforms/MolFragmenter.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In function ‘RDKit::ROMol* RDKit::MolFragmenter::fragmentOnBonds(const RDKit::ROMol&, const std::vector&, bool, const std::vector >*, const std::vector*, std::vector*)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /<>/Code/RDGeneral/RDLog.h:17, from /<>/Code/RDGeneral/Invariant.h:22, from /<>/Code/GraphMol/RDKitBase.h:21, from /<>/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: /usr/include/c++/9/bits/stl_algo.h: In function ‘RDKit::SparseIntVect* RDKit::getUnfoldedRDKFingerprintMol(const RDKit::ROMol&, unsigned int, unsigned int, bool, bool, bool, std::vector*, const std::vector*, std::vector >*, std::map > >*)’: /usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 162 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Atom.h:26, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator > > >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /<>/Code/GraphMol/Fingerprints/Fingerprints.cpp:812:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 812 | } | ^ [ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /<>/Code/GraphMol/Fingerprints/PatternFingerprints.cpp [ 41%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 41%] Built target ChemTransforms make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Subgraphs /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake --color= Scanning dependencies of target testSubgraphs2 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 42%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/Subgraphs/test2.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/Catalogs/Catalog.h:18, from /<>/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, from /<>/Code/GraphMol/FilterCatalog/FilterCatalog.cpp:32: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void boost::archive::detail::iserializer::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::text_iarchive; T = RDKit::FilterCatalogEntry]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 42%] Linking CXX executable testSubgraphs2 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread [ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /<>/Code/GraphMol/Fingerprints/MorganFingerprints.cpp make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 42%] Built target testSubgraphs2 make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Subgraphs /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= Scanning dependencies of target testSubgraphs1 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 42%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/<>/External/boost-numeric-bindings -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/Subgraphs/test1.cpp [ 42%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /<>/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp [ 43%] Linking CXX executable smaTest1 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 43%] Built target smaTest1 make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FragCatalog /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target FragCatalog make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 44%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp:14: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, T&) [with T = std::__cxx11::basic_string]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 44%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FragCatalog/FragCatGenerator.cpp [ 44%] Linking CXX executable testSubgraphs1 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 44%] Built target testSubgraphs1 make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/PartialCharges /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= Scanning dependencies of target testPartialCharges make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 44%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /<>/Code/GraphMol/PartialCharges/test1.cpp [ 45%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Fingerprints/AtomPairs.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h:36, from /<>/Code/GraphMol/FilterCatalog/Filters.h:36, from /<>/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp:32: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 45%] Linking CXX executable testPartialCharges cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/Catalogs/Catalog.h:18, from /<>/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 45%] Built target testPartialCharges make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolChemicalFeatures /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target MolChemicalFeatures make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 45%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp In file included from /usr/include/c++/9/set:60, from /usr/include/boost/graph/adjacency_list.hpp:19, from /<>/Code/Catalogs/Catalog.h:18, from /<>/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:11: /usr/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /usr/include/boost/detail/container_fwd.hpp:94, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_set.hpp:18, from /usr/include/boost/unordered_set.hpp:17, from /usr/include/boost/graph/adjacency_list.hpp:21, from /<>/Code/Catalogs/Catalog.h:18, from /<>/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:11: /usr/include/c++/9/bits/stl_map.h: In function ‘unsigned int RDKit::addOrder1Paths(RDKit::PATH_LIST&, const RDKit::ROMol&, RDKit::FragCatalog*, RDKit::DOUBLE_INT_MAP&, const MatchVectType&)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 45%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/FilterCatalogRunner.cpp.o -c /<>/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/Catalogs/Catalog.h:18, from /<>/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In function ‘unsigned int RDKit::addHigherOrderPaths(const INT_PATH_LIST_MAP&, const RDKit::ROMol&, RDKit::FragCatalog*, RDKit::DOUBLE_INT_MAP&, const MatchVectType&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /usr/include/boost/detail/container_fwd.hpp:94, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_set.hpp:18, from /usr/include/boost/unordered_set.hpp:17, from /usr/include/boost/graph/adjacency_list.hpp:21, from /<>/Code/Catalogs/Catalog.h:18, from /<>/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:11: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/set:60, from /<>/Code/Query/SetQuery.h:13, from /<>/Code/Query/QueryObjects.h:29, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Fingerprints/AtomPairs.cpp:11: /usr/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Atom.h:26, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Fingerprints/AtomPairs.cpp:11: /usr/include/c++/9/bits/stl_map.h: In function ‘RDKit::SparseIntVect* RDKit::AtomPairs::getTopologicalTorsionFingerprint(const RDKit::ROMol&, unsigned int, const std::vector*, const std::vector*, const std::vector*, bool)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 45%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp /usr/include/c++/9/bits/stl_map.h: In function ‘void RDKit::AtomPairs::{anonymous}::TorsionFpCalc(T*, const RDKit::ROMol&, unsigned int, unsigned int, const std::vector*, const std::vector*, const std::vector*, bool) [with T = RDKit::SparseIntVect]’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 45%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/MACCS.cpp.o -c /<>/Code/GraphMol/Fingerprints/MACCS.cpp [ 45%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/FragCatalog/FragCatParams.h:16, from /<>/Code/GraphMol/FragCatalog/FragCatalogEntry.h:14, from /<>/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 46%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FilterCatalog/FilterMatchers.cpp [ 46%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FragCatalog/FragCatParams.cpp [ 46%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp [ 46%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp [ 46%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp [ 46%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FragCatalog/FragFPGenerator.cpp [ 46%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp In file included from /usr/include/c++/9/map:60, from /<>/Code/DataStructs/SparseIntVect.h:15, from /<>/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:11: /usr/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/DataStructs/SparseIntVect.h:15, from /<>/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:11: /usr/include/c++/9/bits/stl_map.h: In member function ‘RDKit::SparseIntVect* RDKit::FingerprintGenerator::getFingerprintHelper(const RDKit::ROMol&, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, uint64_t) const [with OutputType = long long unsigned int]’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/set:60, from /usr/include/boost/graph/adjacency_list.hpp:19, from /<>/Code/Catalogs/Catalog.h:18, from /<>/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:11: /usr/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /usr/include/boost/detail/container_fwd.hpp:94, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_set.hpp:18, from /usr/include/boost/unordered_set.hpp:17, from /usr/include/boost/graph/adjacency_list.hpp:21, from /<>/Code/Catalogs/Catalog.h:18, from /<>/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:11: /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const FragCatalog&, const MatchVectType&, ExplicitBitVect*)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 46%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:15, from /<>/Code/GraphMol/MolChemicalFeatures/FeatureParser.h:17, from /<>/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 721 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 46%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/Catalogs/Catalog.h:18, from /<>/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, from /<>/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h:36, from /<>/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp:33: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2019.09.1 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.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2019.09.1 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 46%] Built target FragCatalog make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ReducedGraphs /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --color= Scanning dependencies of target ReducedGraphs make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 46%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DReducedGraphs_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp /usr/include/c++/9/bits/vector.tcc: In function ‘void RDKit::{anonymous}::hierarchy_create()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 46%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 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.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/include/c++/9/bits/vector.tcc: In function ‘RDKit::MolChemicalFeatureDef* RDKit::Local::parseFeatureDef(std::istream&, const string&, unsigned int&, const std::map, std::__cxx11::basic_string >&)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:15, from /<>/Code/GraphMol/MolChemicalFeatures/FeatureParser.h:17, from /<>/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:11: /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 1662 | _M_range_insert(__pos, __first, __last, | ^~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 46%] Built target FilterCatalog make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/SLNParse /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= Scanning dependencies of target testSLNParse make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 46%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/SLNParse/test.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 46%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2019.09.1 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.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2019.09.1 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 46%] Built target MolChemicalFeatures make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/SLNParse/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= Scanning dependencies of target rdSLNParse make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 46%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp [ 46%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Fingerprints/MorganGenerator.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 46%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2019.09.1 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2019.09.1 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 46%] Built target ReducedGraphs make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= Scanning dependencies of target rdchem make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/rdchem.cpp [ 46%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 46%] Built target rdSLNParse make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ForceFieldHelpers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target ForceFieldHelpers make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 46%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp [ 46%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp [ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp [ 47%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Fingerprints/FingerprintUtil.cpp [ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp [ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/Table.cpp [ 47%] Linking CXX executable testSLNParse cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread [ 48%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 48%] Built target testSLNParse make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolChemicalFeatures/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolChemicalFeatures make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 49%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp [ 49%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2019.09.1 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/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.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 49%] Built target Fingerprints make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ReducedGraphs /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake --color= Scanning dependencies of target testReducedGraphs make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 49%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/ReducedGraphs/test1.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 49%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp [ 49%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/Atom.cpp [ 49%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp [ 49%] Linking CXX executable testReducedGraphs cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 49%] Built target testReducedGraphs make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ReducedGraphs/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= Scanning dependencies of target rdReducedGraphs make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 50%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp [ 50%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp [ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 50%] Built target rdReducedGraphs make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/SubstructLibrary /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= Scanning dependencies of target SubstructLibrary make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 50%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp [ 50%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp [ 50%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /<>/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp [ 50%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/Wrap/Atom.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2019.09.1 ../../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread [ 50%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 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.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 50%] Built target rdMolChemicalFeatures cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Fingerprints/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= Scanning dependencies of target rdFingerprintGenerator make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 50%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp [ 50%] Built target ForceFieldHelpers make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolAlign /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake --color= Scanning dependencies of target MolAlign make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 50%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolAlign/AlignMolecules.cpp [ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/Bond.cpp [ 50%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2019.09.1 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2019.09.1 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 50%] Built target SubstructLibrary make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/DistGeom /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/DistGeom /<>/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= Scanning dependencies of target DistGeometry make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 50%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DistGeom/DistGeomUtils.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/Numerics/Vector.h:15, from /<>/Code/Numerics/Matrix.h:15, from /<>/Code/Numerics/SquareMatrix.h:14, from /<>/Code/Geometry/Transform3D.h:16, from /<>/Code/GraphMol/MolAlign/AlignMolecules.h:14, from /<>/Code/GraphMol/MolAlign/AlignMolecules.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 50%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/O3AAlignMolecules.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/O3AAlignMolecules.cpp.o -c /<>/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp [ 50%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DistGeom/TriangleSmooth.cpp [ 50%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DistGeom/DistViolationContrib.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/Wrap/Bond.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 50%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2019.09.1 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o CMakeFiles/MolAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 50%] Built target MolAlign make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/ForceField/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/ForceField/Wrap /<>/obj-arm-linux-gnueabihf/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= Scanning dependencies of target rdForceField make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 50%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/ForceField/Wrap/ForceField.cpp [ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 50%] Built target rdFingerprintGenerator make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ForceFieldHelpers/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target rdForceFieldHelpers make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 50%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp [ 50%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DistGeom/ChiralViolationContrib.cpp [ 51%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/Mol.cpp [ 52%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /<>/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2019.09.1 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.1.2019.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2019.09.1 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 52%] Built target DistGeometry [ 52%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/Conformer.cpp /<>/Code/ForceField/Wrap/ForceField.cpp: In member function ‘double ForceFields::PyForceField::calcEnergyWithPos(const boost::python::api::object&)’: /<>/Code/ForceField/Wrap/ForceField.cpp:135:12: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 135 | c[i] = python::extract(pos[i]); /<>/Code/ForceField/Wrap/ForceField.cpp: In member function ‘PyObject* ForceFields::PyForceField::calcGradWithPos(const boost::python::api::object&)’: /<>/Code/ForceField/Wrap/ForceField.cpp:169:12: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 169 | c[i] = python::extract(pos[i]); [ 52%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 52%] Built target rdForceFieldHelpers make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Depictor /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= Scanning dependencies of target Depictor make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 52%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Depictor/RDDepictor.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/Wrap/Conformer.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/Wrap/Conformer.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/Wrap/Conformer.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/Wrap/Conformer.cpp:21: /<>/Code/RDBoost/PySequenceHolder.h: In member function ‘T PySequenceHolder::operator[](unsigned int) const [with T = double]’: /<>/Code/RDBoost/PySequenceHolder.h:68:9: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/Wrap/Conformer.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::SetAtomPos(RDKit::Conformer*, unsigned int, boost::python::api::object)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/Depictor/RDDepictor.cpp:12: /<>/Code/GraphMol/Depictor/EmbeddedFrag.h: In member function ‘RDDepict::EmbeddedAtom RDDepict::EmbeddedFrag::GetEmbeddedAtom(unsigned int) const’: /<>/Code/GraphMol/Depictor/EmbeddedFrag.h:314:18: warning: implicitly-declared ‘RDDepict::EmbeddedAtom::EmbeddedAtom(const RDDepict::EmbeddedAtom&)’ is deprecated [-Wdeprecated-copy] 314 | return posi->second; | ^~~~~~ /<>/Code/GraphMol/Depictor/EmbeddedFrag.h:59:17: note: because ‘RDDepict::EmbeddedAtom’ has user-provided ‘RDDepict::EmbeddedAtom& RDDepict::EmbeddedAtom::operator=(const RDDepict::EmbeddedAtom&)’ 59 | EmbeddedAtom &operator=(const EmbeddedAtom &other) { | ^~~~~~~~ [ 52%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/RingInfo.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Depictor/RDDepictor.h:15, from /<>/Code/GraphMol/Depictor/RDDepictor.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Depictor/RDDepictor.h:15, from /<>/Code/GraphMol/Depictor/RDDepictor.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘unsigned int RDDepict::copyCoordinate(RDKit::ROMol&, std::__cxx11::list&, bool)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘unsigned int RDKit::CoordGen::addCoords(T&, const RDKit::CoordGen::CoordGenParams*) [with T = RDKit::ROMol]’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘unsigned int RDDepict::compute2DCoords(RDKit::ROMol&, const INT_POINT2D_MAP*, bool, bool, unsigned int, unsigned int, int, bool, bool)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 53%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /<>/obj-arm-linux-gnueabihf/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/Wrap/Mol.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 53%] Built target rdForceField make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/External/CoordGen/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/External/CoordGen/Wrap /<>/obj-arm-linux-gnueabihf/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake --color= Scanning dependencies of target rdCoordGen make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 53%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o cd /<>/obj-arm-linux-gnueabihf/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCoordGen_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /<>/External/CoordGen/Wrap/rdCoordGen.cpp [ 53%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Depictor/EmbeddedFrag.cpp In file included from /<>/Code/GraphMol/Depictor/EmbeddedFrag.cpp:17: /<>/Code/GraphMol/Depictor/EmbeddedFrag.h: In member function ‘RDDepict::EmbeddedAtom RDDepict::EmbeddedFrag::GetEmbeddedAtom(unsigned int) const’: /<>/Code/GraphMol/Depictor/EmbeddedFrag.h:314:18: warning: implicitly-declared ‘RDDepict::EmbeddedAtom::EmbeddedAtom(const RDDepict::EmbeddedAtom&)’ is deprecated [-Wdeprecated-copy] 314 | return posi->second; | ^~~~~~ /<>/Code/GraphMol/Depictor/EmbeddedFrag.h:59:17: note: because ‘RDDepict::EmbeddedAtom’ has user-provided ‘RDDepict::EmbeddedAtom& RDDepict::EmbeddedAtom::operator=(const RDDepict::EmbeddedAtom&)’ 59 | EmbeddedAtom &operator=(const EmbeddedAtom &other) { | ^~~~~~~~ /<>/Code/GraphMol/Depictor/EmbeddedFrag.cpp: In member function ‘void RDDepict::EmbeddedFrag::addAtomToAtomWithAng(unsigned int, unsigned int)’: /<>/Code/GraphMol/Depictor/EmbeddedFrag.cpp:710:40: warning: implicitly-declared ‘RDDepict::EmbeddedAtom::EmbeddedAtom(const RDDepict::EmbeddedAtom&)’ is deprecated [-Wdeprecated-copy] 710 | EmbeddedAtom refAtom = d_eatoms[toAid]; | ^ In file included from /<>/Code/GraphMol/Depictor/EmbeddedFrag.cpp:17: /<>/Code/GraphMol/Depictor/EmbeddedFrag.h:59:17: note: because ‘RDDepict::EmbeddedAtom’ has user-provided ‘RDDepict::EmbeddedAtom& RDDepict::EmbeddedAtom::operator=(const RDDepict::EmbeddedAtom&)’ 59 | EmbeddedAtom &operator=(const EmbeddedAtom &other) { | ^~~~~~~~ /<>/Code/GraphMol/Depictor/EmbeddedFrag.cpp: In member function ‘void RDDepict::EmbeddedFrag::addAtomToAtomWithNoAng(unsigned int, unsigned int)’: /<>/Code/GraphMol/Depictor/EmbeddedFrag.cpp:781:40: warning: implicitly-declared ‘RDDepict::EmbeddedAtom::EmbeddedAtom(const RDDepict::EmbeddedAtom&)’ is deprecated [-Wdeprecated-copy] 781 | EmbeddedAtom refAtom = d_eatoms[toAid]; | ^ In file included from /<>/Code/GraphMol/Depictor/EmbeddedFrag.cpp:17: /<>/Code/GraphMol/Depictor/EmbeddedFrag.h:59:17: note: because ‘RDDepict::EmbeddedAtom’ has user-provided ‘RDDepict::EmbeddedAtom& RDDepict::EmbeddedAtom::operator=(const RDDepict::EmbeddedAtom&)’ 59 | EmbeddedAtom &operator=(const EmbeddedAtom &other) { | ^~~~~~~~ [ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/EditableMol.cpp In file included from /usr/include/c++/9/map:60, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Depictor/EmbeddedFrag.cpp:10: /usr/include/c++/9/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2187:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2187 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Depictor/EmbeddedFrag.cpp:10: /usr/include/c++/9/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = RDDepict::EmbeddedAtom; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::reflectIfNecessaryThirdPt(RDDepict::EmbeddedFrag&, unsigned int, unsigned int, unsigned int)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::reflectIfNecessaryDensity(RDDepict::EmbeddedFrag&, unsigned int, unsigned int)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘RDGeom::Transform2D RDDepict::EmbeddedFrag::computeTwoAtomTrans(unsigned int, unsigned int, const INT_POINT2D_MAP&)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘std::vector > RDDepict::EmbeddedFrag::findCollisions(const double*, bool)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::openAngles(const double*, unsigned int, unsigned int)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::updateNewNeighs(unsigned int)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In constructor ‘RDDepict::EmbeddedFrag::EmbeddedFrag(unsigned int, const RDKit::ROMol*)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::addAtomToAtomWithNoAng(unsigned int, unsigned int)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/map:60, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Depictor/EmbeddedFrag.cpp:10: /usr/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Depictor/EmbeddedFrag.cpp:10: /usr/include/c++/9/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = unsigned int; _Tp = RDDepict::EmbeddedAtom; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::permuteBonds(unsigned int, unsigned int, unsigned int)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::initFromRingCoords(const INT_VECT&, const INT_POINT2D_MAP&)’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/External/CoordGen/Wrap/rdCoordGen.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/External/CoordGen/Wrap/rdCoordGen.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_map.h: In member function ‘RDGeom::Transform2D RDDepict::EmbeddedFrag::computeOneAtomTrans(unsigned int, const RDDepict::EmbeddedFrag&)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::addAtomToAtomWithAng(unsigned int, unsigned int)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::addNonRingAtom(unsigned int, unsigned int)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_vector.h: In function ‘unsigned int RDKit::CoordGen::addCoords(T&, const RDKit::CoordGen::CoordGenParams*) [with T = RDKit::ROMol]’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::reflectIfNecessaryCisTrans(RDDepict::EmbeddedFrag&, unsigned int, unsigned int, unsigned int)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::computeNbrsAndAng(unsigned int, const INT_VECT&)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /<>/Code/GraphMol/Conformer.h:14, from /<>/Code/GraphMol/RDKitBase.h:25, from /<>/External/CoordGen/Wrap/rdCoordGen.cpp:17: /<>/Code/Geometry/point.h: In function ‘void RDKit::{anonymous}::SetCoordMap(RDKit::CoordGen::CoordGenParams*, boost::python::dict&)’: /<>/Code/Geometry/point.h:293:15: warning: ‘*((void*)(&)+16).RDGeom::Point2D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 293 | x = other.x; | ~~~~~~^ /usr/include/c++/9/bits/stl_map.h: In constructor ‘RDDepict::EmbeddedFrag::EmbeddedFrag(const RDKit::ROMol*, const INT_POINT2D_MAP&)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::mergeWithCommon(RDDepict::EmbeddedFrag&, RDKit::INT_VECT&)’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::mergeFragsWithComm(std::__cxx11::list&)’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::expandEfrag(RDKit::INT_LIST&, std::__cxx11::list&)’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::flipAboutBond(unsigned int, bool)’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::mergeRing(const RDDepict::EmbeddedFrag&, unsigned int, const INT_VECT&)’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::removeCollisionsShortenBonds()’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 53%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so cd /<>/obj-arm-linux-gnueabihf/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 53%] Built target rdCoordGen make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/DistGeomHelpers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target DistGeomHelpers make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 54%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp /usr/include/c++/9/bits/stl_map.h: In member function ‘void RDDepict::EmbeddedFrag::randomSampleFlipsAndPermutations(unsigned int, unsigned int, int, const DOUBLE_SMART_PTR*, double, bool)’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 54%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Depictor/DepictUtils.cpp [ 54%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/MonomerInfo.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Depictor/DepictUtils.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Depictor/DepictUtils.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In function ‘RDDepict::INT_PAIR_VECT RDDepict::findBondsPairsToPermuteDeg4(const RDGeom::Point2D&, const INT_VECT&, const VECT_C_POINT&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 54%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/DistGeomHelpers/Embedder.cpp [ 54%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp [ 54%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2019.09.1 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 54%] Built target Depictor make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/DistGeom /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/DistGeom /<>/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= Scanning dependencies of target testDistGeom make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 54%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/DistGeom/testDistGeom.cpp [ 55%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/MolBundle.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Geometry/point.h:16, from /<>/Code/GraphMol/DistGeomHelpers/Embedder.h:16, from /<>/Code/GraphMol/DistGeomHelpers/Embedder.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Geometry/point.h:16, from /<>/Code/GraphMol/DistGeomHelpers/Embedder.h:16, from /<>/Code/GraphMol/DistGeomHelpers/Embedder.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 55%] Linking CXX executable testDistGeom cd /<>/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2019.09.1 ../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 55%] Built target testDistGeom make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/DistGeom/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap /<>/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= Scanning dependencies of target DistGeom make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 55%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/DistGeom/Wrap/DistGeom.cpp /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::DGeomHelpers::detail::embedHelper_(int, int, RDKit::DGeomHelpers::detail::EmbedArgs*, const RDKit::DGeomHelpers::EmbedParameters*)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 55%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/StereoGroup.cpp [ 55%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2019.09.1 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2019.09.1 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 55%] Built target DistGeomHelpers [ 55%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/SubstanceGroup.cpp [ 55%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /<>/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 55%] Built target DistGeom make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --color= Scanning dependencies of target FileParsers make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/Mol2FileParser.cpp /<>/Code/GraphMol/Wrap/SubstanceGroup.cpp: In function ‘void RDKit::{anonymous}::addBracketHelper(RDKit::SubstanceGroup&, boost::python::api::object)’: /<>/Code/GraphMol/Wrap/SubstanceGroup.cpp:55:16: warning: unused variable ‘i’ [-Wunused-variable] 55 | unsigned int i = 0; | ^ [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/MolFileParser.cpp [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/MolSGroupParsing.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/FileParsers/FileParsers.h:14, from /<>/Code/GraphMol/FileParsers/Mol2FileParser.cpp:37: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/FileParsers/FileParsers.h:14, from /<>/Code/GraphMol/FileParsers/Mol2FileParser.cpp:37: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/FileParsers/FileParsers.h:14, from /<>/Code/GraphMol/FileParsers/Mol2FileParser.cpp:37: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, T&) [with T = std::__cxx11::basic_string]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/Conformer.h:14, from /<>/Code/GraphMol/RDKitBase.h:25, from /<>/Code/GraphMol/Wrap/SubstanceGroup.cpp:17: /<>/Code/Geometry/point.h:56:31: warning: ‘*((void*)(&)+16).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /<>/Code/Geometry/point.h:56:43: warning: ‘*((void*)(&)+16).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /<>/Code/Geometry/point.h:56:55: warning: ‘*((void*)(&)+16).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/GraphMol/Wrap/SubstanceGroup.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/FileParsers/FileParsers.h:14, from /<>/Code/GraphMol/FileParsers/MolSGroupParsing.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/FileParsers/FileParsers.h:14, from /<>/Code/GraphMol/FileParsers/Mol2FileParser.cpp:37: /usr/include/c++/9/bits/stl_vector.h: In function ‘RDKit::RWMol* RDKit::Mol2DataStreamToMol(std::istream*, bool, bool, RDKit::Mol2Type, bool)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/FileParsers/MolFileParser.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/FileParsers/MolFileParser.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/FileParsers/MolFileParser.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/MolFileStereochem.cpp [ 56%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 56%] Built target rdchem [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/MolFileWriter.cpp In file included from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function ‘std::string RDKit::SGroupWriting::BuildV2000SDSLines(const RDKit::ROMol&)’: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: ‘%3d’ directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/9/cstdio:42, from /usr/include/c++/9/ext/string_conversions.h:43, from /usr/include/c++/9/bits/basic_string.h:6493, from /usr/include/c++/9/string:55, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iterator:64, 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:24, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function ‘std::string RDKit::SGroupWriting::BuildV2000StringPropLines(unsigned int, const RDKit::ROMol&, const string&, const string&, unsigned int)’: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: ‘%3d’ directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/9/cstdio:42, from /usr/include/c++/9/ext/string_conversions.h:43, from /usr/include/c++/9/bits/basic_string.h:6493, from /usr/include/c++/9/string:55, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iterator:64, 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:24, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function ‘std::string RDKit::SGroupWriting::BuildV2000STYLines(const RDKit::ROMol&)’: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: ‘%3d’ directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/9/cstdio:42, from /usr/include/c++/9/ext/string_conversions.h:43, from /usr/include/c++/9/bits/basic_string.h:6493, from /usr/include/c++/9/string:55, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iterator:64, 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:24, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function ‘std::string RDKit::SGroupWriting::BuildV2000SBTLines(const RDKit::ROMol&)’: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: ‘%3d’ directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/9/cstdio:42, from /usr/include/c++/9/ext/string_conversions.h:43, from /usr/include/c++/9/bits/basic_string.h:6493, from /usr/include/c++/9/string:55, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iterator:64, 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:24, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: ‘%3d’ directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/9/cstdio:42, from /usr/include/c++/9/ext/string_conversions.h:43, from /usr/include/c++/9/bits/basic_string.h:6493, from /usr/include/c++/9/string:55, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iterator:64, 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:24, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/FileParsers/MolFileParser.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In function ‘bool RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function ‘std::string RDKit::SGroupWriting::BuildV2000SAPLines(int, const RDKit::SubstanceGroup&)’: /<>/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); | ^~~ /<>/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++/9/cstdio:42, from /usr/include/c++/9/ext/string_conversions.h:43, from /usr/include/c++/9/bits/basic_string.h:6493, from /usr/include/c++/9/string:55, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iterator:64, 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:24, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/arm-linux-gnueabihf/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function ‘std::string RDKit::SGroupWriting::BuildV2000SNCLines(const RDKit::ROMol&)’: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: ‘%3d’ directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/9/cstdio:42, from /usr/include/c++/9/ext/string_conversions.h:43, from /usr/include/c++/9/bits/basic_string.h:6493, from /usr/include/c++/9/string:55, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iterator:64, 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:24, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function ‘std::string RDKit::SGroupWriting::BuildV2000SLBLines(const RDKit::ROMol&)’: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: ‘%3d’ directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/9/cstdio:42, from /usr/include/c++/9/ext/string_conversions.h:43, from /usr/include/c++/9/bits/basic_string.h:6493, from /usr/include/c++/9/string:55, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iterator:64, 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:24, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function ‘std::string RDKit::SGroupWriting::BuildV2000SPLLines(const RDKit::ROMol&)’: /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: ‘%3d’ directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /<>/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/9/cstdio:42, from /usr/include/c++/9/ext/string_conversions.h:43, from /usr/include/c++/9/bits/basic_string.h:6493, from /usr/include/c++/9/string:55, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iterator:64, 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:24, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /<>/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/FileParsers/MolFileStereochem.h:14, from /<>/Code/GraphMol/FileParsers/MolFileStereochem.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::{anonymous}::ParseV3000AtomBlock(std::istream*, unsigned int&, unsigned int, RDKit::RWMol*, RDKit::Conformer*)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘void RDKit::ClearSingleBondDirFlags(RDKit::ROMol&)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/SDMolSupplier.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/FileParsers/FileParsers.h:14, from /<>/Code/GraphMol/FileParsers/MolFileWriter.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /<>/Code/RDGeneral/RDLog.h:17, from /<>/Code/RDGeneral/Invariant.h:22, from /<>/Code/RDGeneral/types.h:27, from /<>/Code/GraphMol/FileParsers/FileParsers.h:14, from /<>/Code/GraphMol/FileParsers/MolFileWriter.cpp:13: /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter >]’: /usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /<>/Code/RDGeneral/RDLog.h:17, from /<>/Code/RDGeneral/Invariant.h:22, from /<>/Code/RDGeneral/types.h:27, from /<>/Code/GraphMol/FileParsers/FileParsers.h:14, from /<>/Code/GraphMol/FileParsers/MolFileWriter.cpp:13: /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /<>/Code/RDGeneral/RDLog.h:17, from /<>/Code/RDGeneral/Invariant.h:22, from /<>/Code/RDGeneral/types.h:27, from /<>/Code/GraphMol/FileParsers/FileParsers.h:14, from /<>/Code/GraphMol/FileParsers/MolFileWriter.cpp:13: /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/FileParsers/FileParsers.h:14, from /<>/Code/GraphMol/FileParsers/MolFileWriter.cpp:13: /usr/include/c++/9/bits/vector.tcc: In function ‘void RDKit::GetMolFileAtomProperties(const RDKit::Atom*, const RDKit::Conformer*, int&, int&, unsigned int&, double&, double&, double&)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /<>/Code/RDGeneral/RDLog.h:17, from /<>/Code/RDGeneral/Invariant.h:22, from /<>/Code/RDGeneral/types.h:27, from /<>/Code/GraphMol/FileParsers/FileParsers.h:14, from /<>/Code/GraphMol/FileParsers/MolFileWriter.cpp:13: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/SDWriter.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/FileParsers/SDMolSupplier.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::fpos<__mbstate_t>&}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/FileParsers/SDMolSupplier.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual RDKit::ROMol* RDKit::SDMolSupplier::next()’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In member function ‘unsigned int RDKit::SDMolSupplier::length()’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In member function ‘void RDKit::SDMolSupplier::moveTo(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/SmilesWriter.cpp [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/TDTMolSupplier.cpp [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/TDTWriter.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/TplFileParser.cpp /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, T&) [with T = std::__cxx11::basic_string]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/TplFileWriter.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/token_functions.hpp:34, from /usr/include/boost/token_iterator.hpp:24, from /usr/include/boost/tokenizer.hpp:20, from /<>/Code/GraphMol/FileParsers/TDTMolSupplier.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/token_functions.hpp:34, from /usr/include/boost/token_iterator.hpp:24, from /usr/include/boost/tokenizer.hpp:20, from /<>/Code/GraphMol/FileParsers/TDTMolSupplier.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/token_functions.hpp:34, from /usr/include/boost/token_iterator.hpp:24, from /usr/include/boost/tokenizer.hpp:20, from /<>/Code/GraphMol/FileParsers/TDTMolSupplier.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, T&) [with T = std::__cxx11::basic_string]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘void RDKit::TDTParseUtils::ParseNumberList(std::string, std::vector&, std::istream*) [with T = double]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/token_functions.hpp:34, from /usr/include/boost/token_iterator.hpp:24, from /usr/include/boost/tokenizer.hpp:20, from /<>/Code/GraphMol/FileParsers/TDTMolSupplier.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘RDKit::ROMol* RDKit::TDTMolSupplier::parseMol(std::string)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/PDBParser.cpp [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/PDBWriter.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/FileParsers/TplFileParser.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/FileParsers/TplFileParser.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/FileParsers/TplFileParser.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/PDBSupplier.cpp In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/FileParsers/TplFileParser.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::ParseTPLAtomLine(std::string, unsigned int, RDKit::RWMol*, RDKit::Conformer*)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘RDKit::Conformer* RDKit::ParseConfData(std::istream*, unsigned int&, RDKit::RWMol*, unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/XYZFileWriter.cpp [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/MaeMolSupplier.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/FileParsers/PDBParser.cpp:16: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/FileParsers/PDBParser.cpp:16: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/FileParsers/PDBParser.cpp:16: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/FileParsers/PDBParser.cpp:16: /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::PDBConformerLine(RDKit::RWMol*, const char*, unsigned int, RDKit::Conformer*&, int&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::PDBAtomLine(RDKit::RWMol*, const char*, unsigned int, unsigned int, std::map&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/ProximityBonds.cpp [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/SequenceParsers.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:13: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/SequenceWriters.cpp In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:13: /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::addAtoms(std::shared_ptr&, RDKit::RWMol&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/BadFileException.h:15, from /<>/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘virtual RDKit::ROMol* RDKit::MaeMolSupplier::next()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FileParsers/SVGParser.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/FileParsers/SequenceParsers.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘RDKit::RWMol* RDKit::FASTAToMol(const char*, bool, int)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/FileParsers/SVGParser.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/FileParsers/SVGParser.cpp:10: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/FileParsers/SVGParser.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/FileParsers/SVGParser.cpp:10: /usr/include/c++/9/bits/stl_vector.h: In function ‘RDKit::RWMol* RDKit::RDKitSVGToMol(std::istream*, bool, bool)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 59%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2019.09.1 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 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 59%] Built target FileParsers make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/External/CoordGen /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/External/CoordGen /<>/obj-arm-linux-gnueabihf/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/ForceField/UFF /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/ForceField/UFF /<>/obj-arm-linux-gnueabihf/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --color= make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/ForceField/MMFF /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/ForceField/MMFF /<>/obj-arm-linux-gnueabihf/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= Scanning dependencies of target testUFFForceField make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' Scanning dependencies of target testCoordGen make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 59%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build cd /<>/obj-arm-linux-gnueabihf/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/ForceField/UFF/testUFFForceField.cpp Scanning dependencies of target testMMFFForceField make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make 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-I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/External/CoordGen/test.cpp [ 59%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/ForceField/MMFF && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/ForceField/MMFF/testMMFFForceField.cpp [ 59%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_tests.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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_tests.cpp.o -c /<>/Code/GraphMol/catch_tests.cpp /<>/Code/GraphMol/catch_tests.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____45()’: /<>/Code/GraphMol/catch_tests.cpp:350:14: warning: unused variable ‘m’ [-Wunused-variable] 350 | auto m = SmilesToMol(pr.first); | ^ /<>/Code/GraphMol/catch_tests.cpp:363:14: warning: unused variable ‘m’ [-Wunused-variable] 363 | auto m = SmilesToMol(pr.first); | ^ /<>/Code/GraphMol/catch_tests.cpp:376:14: warning: unused variable ‘m’ [-Wunused-variable] 376 | auto m = SmilesToMol(pr.first); | ^ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/External/CoordGen/test.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/External/CoordGen/test.cpp:13: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/External/CoordGen/test.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/External/CoordGen/test.cpp:13: /usr/include/c++/9/bits/stl_vector.h: In function ‘unsigned int RDKit::CoordGen::addCoords(T&, const RDKit::CoordGen::CoordGenParams*) [with T = RDKit::ROMol]’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/External/CoordGen/test.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, const char*)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/ForceField/MMFF/testMMFFForceField.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘void testMMFFTorsionConstraints()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 59%] Linking CXX executable testUFFForceField cd /<>/obj-arm-linux-gnueabihf/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 59%] Built target testUFFForceField make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolTest1 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 59%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/test1.cpp [ 59%] Linking CXX executable testCoordGen cd /<>/obj-arm-linux-gnueabihf/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../lib/libRDKitDepictor.so.1.2019.09.1 ../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../lib/libRDKitAlignment.so.1.2019.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 59%] Built target testCoordGen make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= Scanning dependencies of target hanoiTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 59%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/hanoitest.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/new_canon.h:14, from /<>/Code/GraphMol/hanoitest.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/test1.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/test1.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/test1.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 59%] Linking CXX executable testMMFFForceField cd /<>/obj-arm-linux-gnueabihf/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2019.09.1 ../../../lib/libRDKitDistGeometry.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, const char*)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 59%] Built target testMMFFForceField make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake --color= Scanning dependencies of target testSGroup make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 59%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/testSGroup.cpp In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/catch_tests.cpp:3: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/catch_tests.cpp:3: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 59%] Linking CXX executable hanoiTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../lib/libRDKitDepictor.so.1.2019.09.1 ../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../lib/libRDKitAlignment.so.1.2019.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 59%] Built target hanoiTest make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= Scanning dependencies of target graphmoltestPicklerGlobalSetting make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 59%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/testPicklerGlobalSettings.cpp In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/catch_tests.cpp:3: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/catch_tests.cpp:3: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/catch_tests.cpp:3: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/testSGroup.cpp:14: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/testPicklerGlobalSettings.cpp:33: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 59%] Linking CXX executable graphmolTest1 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../lib/libRDKitDepictor.so.1.2019.09.1 ../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../lib/libRDKitAlignment.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 59%] Built target graphmolTest1 make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolMolOpsTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 59%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/molopstest.cpp [ 60%] Linking CXX executable testSGroup cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../lib/libRDKitDepictor.so.1.2019.09.1 ../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../lib/libRDKitAlignment.so.1.2019.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 60%] Built target testSGroup make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake --color= Scanning dependencies of target graphmoltestChirality make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 60%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/testChirality.cpp [ 60%] Linking CXX executable graphmoltestPicklerGlobalSetting cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../lib/libRDKitDepictor.so.1.2019.09.1 ../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../lib/libRDKitAlignment.so.1.2019.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 60%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= Scanning dependencies of target graphmoltestPickler make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 60%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/testPickler.cpp In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/catch_tests.cpp:3: /usr/include/c++/9/bits/stl_vector.h: In function ‘void ____C_A_T_C_H____T_E_S_T____35()’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/catch_tests.cpp:3: /usr/include/c++/9/bits/vector.tcc: In function ‘void ____C_A_T_C_H____T_E_S_T____7()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/molopstest.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/molopstest.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In member function ‘void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/molopstest.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/testPickler.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/testPickler.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/testPickler.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 60%] Linking CXX executable graphmolTestsCatch cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/graphmolTestsCatch.dir/catch_tests.cpp.o -o graphmolTestsCatch ../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../lib/libRDKitDepictor.so.1.2019.09.1 ../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../lib/libRDKitAlignment.so.1.2019.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 60%] Built target graphmolTestsCatch make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= Scanning dependencies of target molBundleTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 60%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/testMolBundle.cpp [ 61%] Linking CXX executable graphmoltestPickler cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../lib/libRDKitDepictor.so.1.2019.09.1 ../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../lib/libRDKitAlignment.so.1.2019.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Built target graphmoltestPickler make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol /<>/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= Scanning dependencies of target resMolSupplierTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/resMolSupplierTest.cpp [ 61%] Linking CXX executable molBundleTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../lib/libRDKitDepictor.so.1.2019.09.1 ../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../lib/libRDKitAlignment.so.1.2019.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Built target molBundleTest make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Depictor /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= Scanning dependencies of target testDepictor make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/Depictor/testDepictor.cpp [ 61%] Linking CXX executable graphmoltestChirality cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../lib/libRDKitDepictor.so.1.2019.09.1 ../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../lib/libRDKitAlignment.so.1.2019.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Built target graphmoltestChirality make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Depictor/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= Scanning dependencies of target rdDepictor make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /<>/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/molopstest.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In function ‘void testIssue212()’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘void testAddConformers()’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 61%] Linking CXX executable resMolSupplierTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../lib/libRDKitDepictor.so.1.2019.09.1 ../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../lib/libRDKitAlignment.so.1.2019.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Built target resMolSupplierTest make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/SmilesParse /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake --color= Scanning dependencies of target cxsmilesTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/SmilesParse/cxsmiles_test.cpp In file included from /usr/include/c++/9/set:60, from /<>/Code/Query/SetQuery.h:13, from /<>/Code/Query/QueryObjects.h:29, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Depictor/testDepictor.cpp:13: /usr/include/c++/9/bits/stl_tree.h: In member function ‘void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2504:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2504 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp:18: /<>/Code/GraphMol/Depictor/EmbeddedFrag.h: In member function ‘RDDepict::EmbeddedAtom RDDepict::EmbeddedFrag::GetEmbeddedAtom(unsigned int) const’: /<>/Code/GraphMol/Depictor/EmbeddedFrag.h:314:18: warning: implicitly-declared ‘RDDepict::EmbeddedAtom::EmbeddedAtom(const RDDepict::EmbeddedAtom&)’ is deprecated [-Wdeprecated-copy] 314 | return posi->second; | ^~~~~~ /<>/Code/GraphMol/Depictor/EmbeddedFrag.h:59:17: note: because ‘RDDepict::EmbeddedAtom’ has user-provided ‘RDDepict::EmbeddedAtom& RDDepict::EmbeddedAtom::operator=(const RDDepict::EmbeddedAtom&)’ 59 | EmbeddedAtom &operator=(const EmbeddedAtom &other) { | ^~~~~~~~ /usr/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Atom.h:26, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Depictor/testDepictor.cpp:13: /usr/include/c++/9/bits/stl_map.h: In function ‘void testIssue2091304()’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In function ‘void testIssue3122141()’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In function ‘void testIssue2303566()’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In function ‘void testIssue3135833()’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In function ‘void test4()’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/set:60, from /<>/Code/Query/SetQuery.h:13, from /<>/Code/Query/QueryObjects.h:29, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Depictor/testDepictor.cpp:13: /usr/include/c++/9/bits/stl_tree.h:1220:2: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 1220 | _M_erase_aux(__position); | ^~~~~~~~~~~~ /usr/include/c++/9/bits/stl_tree.h:1220:2: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 1220 | _M_erase_aux(__position); | ^~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Atom.h:26, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Depictor/testDepictor.cpp:13: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/set:60, from /<>/Code/Query/SetQuery.h:13, from /<>/Code/Query/QueryObjects.h:29, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Depictor/testDepictor.cpp:13: /usr/include/c++/9/bits/stl_tree.h:1220:2: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 1220 | _M_erase_aux(__position); | ^~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘void testAddHsCoords()’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/Depictor/RDDepictor.h:16, from /<>/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp:17: /<>/Code/Geometry/point.h: In function ‘unsigned int RDDepict::Compute2DCoords(RDKit::ROMol&, bool, bool, boost::python::dict&, unsigned int, unsigned int, int, bool, double, bool)’: /<>/Code/Geometry/point.h:293:15: warning: ‘*((void*)(&)+16).RDGeom::Point2D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 293 | x = other.x; | ~~~~~~^ [ 61%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Built target rdDepictor make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/SmilesParse /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake --color= [ 61%] Linking CXX executable testDepictor cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 Scanning dependencies of target smiTestCatch make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/SmilesParse/catch_tests.cpp make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Built target testDepictor make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/SmilesParse /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake --color= Scanning dependencies of target smiTest1 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/SmilesParse/test.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/molopstest.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setPODVal(const string&, T) [with T = int]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 61%] Linking CXX executable cxsmilesTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Built target cxsmilesTest make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= Scanning dependencies of target testMol2ToMol make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/FileParsers/testMol2ToMol.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/SmilesParse/test.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 61%] Linking CXX executable testMol2ToMol cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake --color= Scanning dependencies of target fileParsersTest1 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/FileParsers/test1.cpp In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/SmilesParse/catch_tests.cpp:14: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/SmilesParse/catch_tests.cpp:14: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/FileParsers/test1.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/FileParsers/test1.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/FileParsers/test1.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/FileParsers/test1.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In function ‘void testIssue2963522()’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 61%] Linking CXX executable graphmolMolOpsTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../lib/libRDKitDepictor.so.1.2019.09.1 ../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../lib/libRDKitAlignment.so.1.2019.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Built target graphmolMolOpsTest make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake --color= Scanning dependencies of target testPropertyLists make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/FileParsers/testPropertyLists.cpp /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, const char*)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘void testBug3525799()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 61%] Linking CXX executable smiTest1 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Built target smiTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake --color= Scanning dependencies of target testMolSupplier make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/FileParsers/testMolSupplier.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/FileParsers/testMolSupplier.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::fpos<__mbstate_t>&}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In function ‘void testGitHub23()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/FileParsers/testMolSupplier.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In function ‘void testSetStreamIndices()’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/FileParsers/testPropertyLists.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/FileParsers/testPropertyLists.cpp:13: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 61%] Linking CXX executable smiTestCatch cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/FileParsers/testPropertyLists.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Built target smiTestCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= Scanning dependencies of target testMolWriter make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/FileParsers/testMolWriter.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/FileParsers/testMolWriter.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/FileParsers/testMolWriter.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/FileParsers/testMolWriter.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 62%] Linking CXX executable testMolSupplier cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitRDStreams.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 62%] Built target testMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake --color= Scanning dependencies of target testTplParser make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/FileParsers/testTpls.cpp [ 63%] Linking CXX executable fileParsersTest1 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 63%] Built target fileParsersTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= Scanning dependencies of target testSequence make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/FileParsers/testSequence.cpp [ 63%] Linking CXX executable testTplParser cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/FileParsers/testMolWriter.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In function ‘void testIssue265()’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 63%] Built target testTplParser make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= Scanning dependencies of target testExtendedStereoParsing make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp [ 63%] Linking CXX executable testSequence cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 63%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= Scanning dependencies of target fileParsersCatchTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/catch_tests.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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_tests.cpp.o -c /<>/Code/GraphMol/FileParsers/catch_tests.cpp [ 63%] Linking CXX executable testMolWriter cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 63%] Built target testMolWriter make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Substruct /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake --color= Scanning dependencies of target substructTestCatch make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/Substruct/catch_tests.cpp [ 63%] Linking CXX executable testExtendedStereoParsing cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 63%] Built target testExtendedStereoParsing make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Substruct /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= Scanning dependencies of target testSubstructMatch make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/Substruct/test1.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Substruct/test1.cpp:17: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 63%] Linking CXX executable testPropertyLists cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 63%] Built target testPropertyLists make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Descriptors /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= Scanning dependencies of target Descriptors make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/Crippen.cpp.o -c /<>/Code/GraphMol/Descriptors/Crippen.cpp /usr/include/c++/9/bits/vector.tcc: In function ‘void test5QueryRoot()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/FileParsers/catch_tests.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/FileParsers/catch_tests.cpp:13: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/Substruct/catch_tests.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/Substruct/catch_tests.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/Descriptors/Crippen.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDKit::Descriptors::CrippenParams&}; _Tp = RDKit::Descriptors::CrippenParams; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/Descriptors/Crippen.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Descriptors::CrippenParamCollection::CrippenParamCollection(const string&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/FileParsers/catch_tests.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/FileParsers/catch_tests.cpp:13: /usr/include/c++/9/bits/stl_vector.h: In member function ‘void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 63%] Linking CXX executable testSubstructMatch cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 63%] Built target testSubstructMatch make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ChemTransforms /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake --color= Scanning dependencies of target chemTransformsTestCatch make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 64%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/ChemTransforms/catch_tests.cpp [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /<>/Code/GraphMol/Descriptors/MolDescriptors.cpp In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/FileParsers/catch_tests.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Descriptors/MolSurf.cpp /usr/include/c++/9/bits/vector.tcc: In function ‘void ____C_A_T_C_H____T_E_S_T____38()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Descriptors/MolSurf.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Descriptors/Lipinski.cpp In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/ChemTransforms/catch_tests.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/ChemTransforms/catch_tests.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ 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-std=gnu++11 -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /<>/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp [ 65%] Linking CXX executable substructTestCatch cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 65%] Built target substructTestCatch make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/ChemTransforms/testChemTransforms.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/Code/GraphMol/ROMol.h:27, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Descriptors/MQN.cpp [ 65%] Linking CXX executable fileParsersCatchTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/fileParsersCatchTest.dir/catch_tests.cpp.o -o fileParsersCatchTest 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/usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 65%] Built target fileParsersCatchTest make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FilterCatalog /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake --color= Scanning dependencies of target filterCatalogTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build make[4]: 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /<>/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Descriptors/Property.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/ChemTransforms/testChemTransforms.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp:33: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, const char*)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘void testFilterCatalogEntry()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Descriptors/Property.h:36, from /<>/Code/GraphMol/Descriptors/Property.cpp:32: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘std::vector RDKit::Descriptors::Properties::computeProperties(const RDKit::ROMol&, bool) const’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 65%] Linking CXX executable filterCatalogTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 65%] Built target filterCatalogTest make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FilterCatalog/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= Scanning dependencies of target rdfiltercatalog make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 65%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Descriptors/AUTOCORR2D.cpp [ 65%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, const char*)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/Data3Ddescriptors.cpp.o -c /<>/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp [ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp [ 66%] Linking CXX executable testChemTransforms cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic 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/usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 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 '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FragCatalog /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target testFragCatalog make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /<>/Code/GraphMol/FragCatalog/test1.cpp [ 66%] Linking CXX executable chemTransformsTestCatch cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 66%] Built target chemTransformsTestCatch make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FragCatalog/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= Scanning dependencies of target rdfragcatalog make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp [ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Descriptors/USRDescriptor.cpp [ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp [ 67%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2019.09.1 CMakeFiles/Descriptors.dir/Crippen.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 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread [ 67%] Linking CXX executable testFragCatalog cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 67%] Built target Descriptors make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Fingerprints /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= Scanning dependencies of target testFingerprintGenerators make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 67%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 67%] Built target testFragCatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Fingerprints /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= Scanning dependencies of target testFingerprints make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 67%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/Fingerprints/test1.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /<>/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /<>/Code/RDGeneral/RDLog.h:17, from /<>/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:11: /usr/include/c++/9/bits/stl_algo.h: In function ‘_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]’: /usr/include/c++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 112 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::FilterCatalogEntry::setProp(const string&, T) [with T = std::__cxx11::basic_string]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘void testAtomPairOutput()’: /usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 162 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 162 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 162 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 162 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 162 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 162 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Fingerprints/test1.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 [ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp In file included from /usr/include/c++/9/set:60, from /<>/Code/Query/SetQuery.h:13, from /<>/Code/Query/QueryObjects.h:29, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:12: /usr/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Atom.h:26, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:12: /usr/include/c++/9/bits/stl_map.h: In function ‘void testRDKitFP()’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In function ‘void testTopologicalTorsionFPOld()’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp [ 67%] Linking CXX executable testFingerprintGenerators cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 67%] Built target testFingerprintGenerators make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Fingerprints /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake --color= Scanning dependencies of target fpTestCatch make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 67%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/Fingerprints/catch_tests.cpp [ 67%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -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.1.2019.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 67%] Built target rdfiltercatalog make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolTransforms /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target testMolTransforms make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 67%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolTransforms/test1.cpp /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::RDProps::clearProp(const string&) const’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolTransforms/test1.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolTransforms/test1.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘void test1Canonicalization()’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 67%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -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.1.2019.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 67%] Built target rdfragcatalog make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ForceFieldHelpers/MMFF /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake --color= Scanning dependencies of target testMMFFForceFieldHelpersMultiThread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 67%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp [ 67%] Linking CXX executable testMolTransforms cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 67%] Built target testMolTransforms make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ForceFieldHelpers/MMFF /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake 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-I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp [ 69%] Linking CXX executable testFingerprints cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic 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/usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 69%] Built target testFingerprints make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ForceFieldHelpers/UFF /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target testUFFForceFieldHelpers make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 69%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp [ 69%] Linking CXX executable testMMFFForceFieldHelpersMultiThread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic 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../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 69%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ForceFieldHelpers/CrystalFF /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= Scanning dependencies of target testCrystalForceField make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 69%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp:15: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp:15: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/Fingerprints/catch_tests.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/Fingerprints/catch_tests.cpp:13: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 70%] Linking CXX executable testCrystalForceField cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2019.09.1 ../../../../lib/libRDKitDistGeometry.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 70%] Built target testCrystalForceField make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/DistGeomHelpers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target testDistGeomHelpers make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 70%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp:15: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp:15: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 70%] Linking CXX executable testMMFFForceFieldHelpers cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2019.09.1 ../../../../lib/libRDKitDistGeometry.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 70%] 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 '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/DistGeomHelpers/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --color= Scanning dependencies of target rdDistGeom make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 71%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 71%] Linking CXX executable testUFFForceFieldHelpers cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2019.09.1 ../../../../lib/libRDKitDistGeometry.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 71%] Built target testUFFForceFieldHelpers make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolAlign /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake --color= Scanning dependencies of target testMolAlign make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 71%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolAlign/testMolAlign.cpp In file included from /usr/include/c++/9/map:60, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/Code/RDBoost/python.h:5, from /<>/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: /usr/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/Conformer.h:14, from /<>/Code/GraphMol/ROMol.h:36, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:17: /<>/Code/Geometry/point.h: In function ‘RDKit::INT_VECT RDKit::EmbedMultipleConfs(RDKit::ROMol&, unsigned int, unsigned int, int, bool, bool, double, bool, unsigned int, double, boost::python::dict&, double, bool, bool, int, bool, bool, bool)’: /<>/Code/Geometry/point.h:85:15: warning: ‘*((void*)(&)+16).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 85 | x = other.x; | ~~~~~~^ In file included from /usr/include/c++/9/map:61, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/Code/RDBoost/python.h:5, from /<>/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /<>/Code/GraphMol/Conformer.h:14, from /<>/Code/GraphMol/ROMol.h:36, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:17: /<>/Code/Geometry/point.h: In function ‘int RDKit::EmbedMolecule(RDKit::ROMol&, unsigned int, int, bool, bool, double, bool, unsigned int, boost::python::dict&, double, bool, bool, bool, bool, bool)’: /<>/Code/Geometry/point.h:85:15: warning: ‘*((void*)(&)+16).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 85 | x = other.x; | ~~~~~~^ In file included from /usr/include/c++/9/map:61, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/Code/RDBoost/python.h:5, from /<>/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/set:60, from /<>/Code/Query/SetQuery.h:13, from /<>/Code/Query/QueryObjects.h:29, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp:13: /usr/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Atom.h:26, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp:13: /usr/include/c++/9/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = int; _Tp = RDGeom::Point3D; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In function ‘void testGithub2246()’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In function ‘void testConstrainedEmbedding()’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In function ‘void testGithub55()’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp:13: /usr/include/c++/9/bits/vector.tcc: In function ‘void testGithub568()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/Numerics/Vector.h:15, from /<>/Code/Numerics/Matrix.h:15, from /<>/Code/Numerics/SquareMatrix.h:14, from /<>/Code/Geometry/Transform3D.h:16, from /<>/Code/GraphMol/MolAlign/AlignMolecules.h:14, from /<>/Code/GraphMol/MolAlign/testMolAlign.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 71%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2019.09.1 ../../../../lib/libRDKitDistGeometry.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 71%] Built target rdDistGeom make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolAlign/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolAlign make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 71%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp [ 71%] Linking CXX executable testDistGeomHelpers cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2019.09.1 ../../../lib/libRDKitDistGeometry.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 71%] Built target testDistGeomHelpers make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolChemicalFeatures /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target testFeatures make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 71%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp [ 72%] Linking CXX executable testMolAlign cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2019.09.1 ../../../lib/libRDKitDistGeometry.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 72%] Built target testMolAlign make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ShapeHelpers /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target testShapeHelpers make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 72%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp /<>/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function ‘RDKit::MolAlign::PyO3A* RDKit::MolAlign::getCrippenO3A(RDKit::ROMol&, RDKit::ROMol&, boost::python::list, boost::python::list, int, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)’: /<>/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:451:40: warning: comparison of integer expressions of different signedness: ‘boost::python::ssize_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 451 | (python::len(prbCrippenContribs) == prbNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /<>/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:466:40: warning: comparison of integer expressions of different signedness: ‘boost::python::ssize_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 466 | (python::len(refCrippenContribs) == refNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /<>/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function ‘boost::python::tuple RDKit::MolAlign::getCrippenO3AForConfs(RDKit::ROMol&, RDKit::ROMol&, int, boost::python::list, boost::python::list, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)’: /<>/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:532:40: warning: comparison of integer expressions of different signedness: ‘boost::python::ssize_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 532 | (python::len(prbCrippenContribs) == prbNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /<>/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:547:40: warning: comparison of integer expressions of different signedness: ‘boost::python::ssize_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 547 | (python::len(refCrippenContribs) == refNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 72%] Linking CXX executable fpTestCatch cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 72%] Built target fpTestCatch make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolCatalog /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target testMolCatalog make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 72%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolCatalog/test1.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:16: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:16: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 72%] Linking CXX executable testShapeHelpers cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 72%] Built target testShapeHelpers make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolCatalog/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolCatalog make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 72%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp In file included from /<>/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:24: /<>/Code/RDBoost/PySequenceHolder.h: In function ‘RDNumeric::DoubleVector* RDKit::_translateWeights(boost::python::api::object)’: /<>/Code/RDBoost/PySequenceHolder.h:68:9: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘void test6()’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘void testGithub2077()’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 72%] Linking CXX executable testFeatures cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 72%] Built target testFeatures make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FMCS /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= Scanning dependencies of target FMCS make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 72%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FMCS/FMCS.cpp [ 72%] Linking CXX executable testMolCatalog cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 72%] Built target testMolCatalog make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolHash /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake --color= Scanning dependencies of target MolHash make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 72%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/MolHash.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/MolHash.cpp.o -c /<>/Code/GraphMol/MolHash/MolHash.cpp [ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 72%] Built target rdMolAlign make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MMPA /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= Scanning dependencies of target MMPA make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 73%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MMPA/MMPA.cpp [ 73%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 73%] Built target rdMolCatalog make -f Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/StructChecker /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/DependInfo.cmake --color= Scanning dependencies of target StructChecker make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 74%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructChecker.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/StructChecker.dir/StructChecker.cpp.o -c /<>/Code/GraphMol/StructChecker/StructChecker.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/MMPA/MMPA.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 74%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/HashToString.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/HashToString.cpp.o -c /<>/Code/GraphMol/MolHash/HashToString.cpp [ 74%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2019.09.1 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2019.09.1 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 74%] Built target MMPA make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Trajectory /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake --color= Scanning dependencies of target trajectoryTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 74%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/Trajectory/trajectoryTest.cpp [ 74%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FMCS/Seed.cpp [ 74%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o -c /<>/Code/GraphMol/StructChecker/StructCheckerOptions.cpp [ 75%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolHash/hashfunctions.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/Trajectory/Trajectory.h:14, from /<>/Code/GraphMol/Trajectory/trajectoryTest.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘void testAddConformersFromTrajectory()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 75%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp [ 76%] Linking CXX executable trajectoryTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 [ 76%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolHash/normalize.cpp make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 76%] Built target trajectoryTest make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/SubstructLibrary /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= Scanning dependencies of target substructLibraryTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 77%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp [ 77%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructureFlags.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/StructChecker.dir/StructureFlags.cpp.o -c /<>/Code/GraphMol/StructChecker/StructureFlags.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolHash/normalize.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::RDProps::clearProp(const string&) const’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 77%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2019.09.1 CMakeFiles/MolHash.dir/MolHash.cpp.o CMakeFiles/MolHash.dir/HashToString.cpp.o CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2019.09.1 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 77%] Built target MolHash make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/SubstructLibrary/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= Scanning dependencies of target rdSubstructLibrary make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 78%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp [ 78%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Utilites.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/StructChecker.dir/Utilites.cpp.o -c /<>/Code/GraphMol/StructChecker/Utilites.cpp [ 78%] Linking CXX executable substructLibraryTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 78%] Built target substructLibraryTest make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolInterchange /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake --color= Scanning dependencies of target molInterchangeTest1 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /<>/Code/GraphMol/MolInterchange/test1.cpp [ 78%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp [ 78%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Pattern.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/StructChecker.dir/Pattern.cpp.o -c /<>/Code/GraphMol/StructChecker/Pattern.cpp [ 79%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FMCS/SubstructMatchCustom.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolInterchange/test1.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 79%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Stereo.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/StructChecker.dir/Stereo.cpp.o -c /<>/Code/GraphMol/StructChecker/Stereo.cpp [ 79%] Linking CXX executable molInterchangeTest1 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 79%] Built target molInterchangeTest1 make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= Scanning dependencies of target rdmolfiles make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/rdmolfiles.cpp [ 80%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2019.09.1 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.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2019.09.1 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 80%] Built target FMCS make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ChemReactions /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake --color= Scanning dependencies of target ChemReactions make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ChemReactions/Reaction.cpp [ 82%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/AtomSymbolMatch.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/StructChecker.dir/AtomSymbolMatch.cpp.o -c /<>/Code/GraphMol/StructChecker/AtomSymbolMatch.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/ChemReactions/Reaction.h:37, from /<>/Code/GraphMol/ChemReactions/Reaction.cpp:33: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2019.09.1 ../../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 82%] Built target rdSubstructLibrary make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp [ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ChemReactions/MDLParser.cpp [ 83%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StripSmallFragments.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/StructChecker.dir/StripSmallFragments.cpp.o -c /<>/Code/GraphMol/StructChecker/StripSmallFragments.cpp [ 83%] Linking CXX executable testAUTOCORR2D cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 83%] Built target testAUTOCORR2D make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Descriptors /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake --color= Scanning dependencies of target testDescriptors make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 83%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /<>/Code/GraphMol/Descriptors/test.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/StructChecker/../MolOps.h:15, from /<>/Code/GraphMol/StructChecker/StripSmallFragments.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 83%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/ReCharge.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/StructChecker.dir/ReCharge.cpp.o -c /<>/Code/GraphMol/StructChecker/ReCharge.cpp [ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/DaylightParser.cpp.o -c /<>/Code/GraphMol/ChemReactions/DaylightParser.cpp [ 83%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Tautomer.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/StructChecker.dir/Tautomer.cpp.o -c /<>/Code/GraphMol/StructChecker/Tautomer.cpp [ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /<>/Code/GraphMol/ChemReactions/ReactionPickler.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/Descriptors/test.cpp:18: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/Wrap/rdmolfiles.cpp:13: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, T&) [with T = std::__cxx11::basic_string]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 83%] Linking CXX shared library ../../../lib/libRDKitStructChecker.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/cmake -E cmake_link_script CMakeFiles/StructChecker.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitStructChecker.so.1 -o ../../../lib/libRDKitStructChecker.so.1.2019.09.1 CMakeFiles/StructChecker.dir/StructChecker.cpp.o CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o CMakeFiles/StructChecker.dir/StructureFlags.cpp.o CMakeFiles/StructChecker.dir/Utilites.cpp.o CMakeFiles/StructChecker.dir/Pattern.cpp.o CMakeFiles/StructChecker.dir/Stereo.cpp.o CMakeFiles/StructChecker.dir/AtomSymbolMatch.cpp.o CMakeFiles/StructChecker.dir/StripSmallFragments.cpp.o CMakeFiles/StructChecker.dir/ReCharge.cpp.o CMakeFiles/StructChecker.dir/Tautomer.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitStructChecker.so.1.2019.09.1 ../../../lib/libRDKitStructChecker.so.1 ../../../lib/libRDKitStructChecker.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 83%] Built target StructChecker make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Descriptors/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolDescriptors make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 83%] Building CXX object Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDescriptors_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp [ 83%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp [ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ChemReactions/ReactionWriter.cpp In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /<>/Code/GraphMol/Descriptors/test.cpp:18: /usr/include/c++/9/bits/stl_vector.h: In function ‘void testProperties()’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/ChemReactions/Reaction.h:37, from /<>/Code/GraphMol/ChemReactions/ReactionWriter.cpp:33: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘void {anonymous}::setRXNRoleOfAllMoleculeAtoms(RDKit::ROMol&, int)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ChemReactions/ReactionDepict.cpp [ 83%] Linking CXX executable testDescriptors cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 83%] Built target testDescriptors make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FMCS /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= Scanning dependencies of target testFMCS make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 83%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/FMCS/testFMCS_Unit.cpp In file included from /<>/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:22: /<>/Code/RDBoost/python_streambuf.h: In constructor ‘boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)’: /<>/Code/RDBoost/python_streambuf.h:186:56: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h:156:58: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)’: /<>/Code/RDBoost/python_streambuf.h:379:16: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 379 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /<>/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp [ 83%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/MaeMolSupplier.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/FMCS/testFMCS_Unit.cpp:48: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/Conformer.h:14, from /<>/Code/GraphMol/ROMol.h:36, from /<>/Code/GraphMol/GraphMol.h:19, from /<>/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:12: /<>/Code/Geometry/point.h: In function ‘boost::python::list {anonymous}::GetUSRDistributionsFromPoints(boost::python::api::object, boost::python::api::object)’: /<>/Code/Geometry/point.h:85:15: warning: ‘*((void*)(&)+16).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 85 | x = other.x; | ~~~~~~^ /<>/Code/Geometry/point.h:86:15: warning: ‘*((void*)(&)+16).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 86 | y = other.y; | ~~~~~~^ /<>/Code/Geometry/point.h:87:15: warning: ‘*((void*)(&)+16).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | z = other.z; | ~~~~~~^ /<>/Code/Geometry/point.h: In function ‘boost::python::list {anonymous}::GetUSRDistributions(boost::python::api::object, boost::python::api::object)’: /<>/Code/Geometry/point.h:85:15: warning: ‘*((void*)(&)+16).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 85 | x = other.x; | ~~~~~~^ /<>/Code/Geometry/point.h:86:15: warning: ‘*((void*)(&)+16).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 86 | y = other.y; | ~~~~~~^ /<>/Code/Geometry/point.h:87:15: warning: ‘*((void*)(&)+16).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | z = other.z; | ~~~~~~^ /<>/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp: In function ‘RDKit::SparseIntVect* RDKit::DifferenceFingerprintChemReaction(const RDKit::ChemicalReaction&, const RDKit::ReactionFingerprintParams&)’: /<>/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp:221:42: warning: implicitly-declared ‘RDKit::SparseIntVect& RDKit::SparseIntVect::operator=(const RDKit::SparseIntVect&)’ is deprecated [-Wdeprecated-copy] 221 | (*res) = *productFP - *reactantFP + *agentFP; | ^~~~~~~ In file included from /<>/Code/GraphMol/Fingerprints/Fingerprints.h:16, from /<>/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp:37: /<>/Code/DataStructs/SparseIntVect.h:38:3: note: because ‘RDKit::SparseIntVect’ has user-provided ‘RDKit::SparseIntVect::SparseIntVect(const RDKit::SparseIntVect&) [with IndexType = unsigned int]’ 38 | SparseIntVect(const SparseIntVect &other) { | ^~~~~~~~~~~~~ /<>/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp:226:28: warning: implicitly-declared ‘RDKit::SparseIntVect& RDKit::SparseIntVect::operator=(const RDKit::SparseIntVect&)’ is deprecated [-Wdeprecated-copy] 226 | (*res) = *productFP - *reactantFP; | ^~~~~~~~~~ In file included from /<>/Code/GraphMol/Fingerprints/Fingerprints.h:16, from /<>/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp:37: /<>/Code/DataStructs/SparseIntVect.h:38:3: note: because ‘RDKit::SparseIntVect’ has user-provided ‘RDKit::SparseIntVect::SparseIntVect(const RDKit::SparseIntVect&) [with IndexType = unsigned int]’ 38 | SparseIntVect(const SparseIntVect &other) { | ^~~~~~~~~~~~~ [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /<>/Code/GraphMol/ChemReactions/ReactionUtils.cpp [ 84%] Linking CXX executable testFMCS cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Built target testFMCS make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FMCS/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= Scanning dependencies of target rdFMCS make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp In file included from /<>/Code/GraphMol/Wrap/MaeMolSupplier.cpp:21: /<>/Code/RDBoost/python_streambuf.h: In constructor ‘boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)’: /<>/Code/RDBoost/python_streambuf.h:186:56: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h:156:58: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)’: /<>/Code/RDBoost/python_streambuf.h:379:16: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 379 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/ChemReactions/Reaction.h:37, from /<>/Code/GraphMol/ChemReactions/ReactionUtils.cpp:34: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/SDMolSupplier.cpp [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /<>/Code/GraphMol/ChemReactions/MoleculeParser.cpp [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/ReactionRunner.cpp.o -c /<>/Code/GraphMol/ChemReactions/ReactionRunner.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/Wrap/SDMolSupplier.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘void RDKit::setStreamIndices(RDKit::SDMolSupplier&, boost::python::api::object)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Built target rdFMCS make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/FMCS/Test /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= Scanning dependencies of target FMCStest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/FMCS/Test/testFMCS.cpp [ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/TDTMolSupplier.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/ChemReactions/Reaction.h:37, from /<>/Code/GraphMol/ChemReactions/ReactionRunner.cpp:33: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /<>/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function ‘std::string testChEMBL_Txt(const char*, double, const char*)’: /<>/Code/GraphMol/FMCS/Test/testFMCS.cpp:501:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wformat=] 501 | fprintf(fres, "%s;%lu;%.1f;%.4f;%u;%u;%s;", test, mols.size(), th, sec, | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /<>/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function ‘void testFileSDF_RandomSet_SMI(const char*, const char*)’: /<>/Code/GraphMol/FMCS/Test/testFMCS.cpp:1173:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wformat=] 1173 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s;", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /<>/Code/GraphMol/FMCS/Test/testFMCS.cpp:1185:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wformat=] 1185 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s\n", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /<>/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function ‘void testFileSDF_RandomSet(const char*, const char*)’: /<>/Code/GraphMol/FMCS/Test/testFMCS.cpp:1287:29: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wformat=] 1287 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /<>/Code/GraphMol/FMCS/Test/testFMCS.cpp:1336:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wformat=] 1336 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /<>/Code/GraphMol/FMCS/Test/testFMCS.cpp:1416:29: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wformat=] 1416 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/ChemReactions/Reaction.h:37, from /<>/Code/GraphMol/ChemReactions/ReactionRunner.cpp:33: /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::ReactionRunnerUtils::generateProductConformers(RDKit::Conformer*, const RDKit::ROMol&, RDKit::ReactionRunnerUtils::ReactantProductAtomMapping*)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/ChemReactions/Reaction.h:37, from /<>/Code/GraphMol/ChemReactions/ReactionRunner.cpp:33: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/FMCS/Test/../../RDKitBase.h:23, from /<>/Code/GraphMol/FMCS/Test/testFMCS.cpp:48: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /<>/Code/GraphMol/ChemReactions/PreprocessRxn.cpp /usr/include/c++/9/bits/vector.tcc: In function ‘void test504()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 [ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/SmilesMolSupplier.cpp make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Built target rdMolDescriptors make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolHash /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake --color= Scanning dependencies of target molHashCatchTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolHash/catch_tests.cpp [ 84%] Linking CXX executable FMCStest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Built target FMCStest make -f Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolHash /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/DependInfo.cmake --color= Scanning dependencies of target testMolHash make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/testMolHash.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolHash.dir/testMolHash.cpp.o -c /<>/Code/GraphMol/MolHash/testMolHash.cpp [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /<>/Code/GraphMol/ChemReactions/SanitizeRxn.cpp [ 84%] Linking CXX executable testMolHash cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolHash.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testMolHash.dir/testMolHash.cpp.o -o testMolHash ../../../lib/libRDKitMolHash.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Built target testMolHash make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolHash/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolHash make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp [ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/SmilesWriter.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/ChemReactions/Reaction.h:37, from /<>/Code/GraphMol/ChemReactions/SanitizeRxn.h:36, from /<>/Code/GraphMol/ChemReactions/SanitizeRxn.cpp:32: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -fpermissive -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /<>/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp [ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2019.09.1 ../../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Built target rdMolHash make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MMPA /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= Scanning dependencies of target testMMPA make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MMPA/MMPA_UnitTest.cpp In file included from /<>/Code/GraphMol/Wrap/SmilesWriter.cpp:20: /<>/Code/RDBoost/python_streambuf.h: In constructor ‘boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)’: /<>/Code/RDBoost/python_streambuf.h:186:56: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h:156:58: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)’: /<>/Code/RDBoost/python_streambuf.h:379:16: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 379 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/SDWriter.cpp In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/MolHash/catch_tests.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/MolHash/catch_tests.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 85%] Linking CXX executable testMMPA cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 85%] Built target testMMPA make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MMPA/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= Scanning dependencies of target rdMMPA make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 85%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp [ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp In file included from /<>/Code/GraphMol/Wrap/SDWriter.cpp:21: /<>/Code/RDBoost/python_streambuf.h: In constructor ‘boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)’: /<>/Code/RDBoost/python_streambuf.h:186:56: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h:156:58: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)’: /<>/Code/RDBoost/python_streambuf.h:379:16: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 379 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/TDTWriter.cpp [ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /<>/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp [ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 86%] Built target rdMMPA make -f Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/StructChecker /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/DependInfo.cmake --color= Scanning dependencies of target testStructChecker make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 86%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/testStructChecker.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testStructChecker.dir/testStructChecker.cpp.o -c /<>/Code/GraphMol/StructChecker/testStructChecker.cpp In file included from /<>/Code/GraphMol/Wrap/TDTWriter.cpp:21: /<>/Code/RDBoost/python_streambuf.h: In constructor ‘boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)’: /<>/Code/RDBoost/python_streambuf.h:186:56: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h:156:58: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)’: /<>/Code/RDBoost/python_streambuf.h:379:16: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 379 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/CompressedSDMolSupplier.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/CompressedSDMolSupplier.cpp.o -c /<>/Code/GraphMol/Wrap/CompressedSDMolSupplier.cpp [ 86%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2019.09.1 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 86%] Built target ChemReactions make -f Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build.make Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/StructChecker/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/DependInfo.cmake --color= Scanning dependencies of target rdStructChecker make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build.make Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 86%] Building CXX object Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/structchecker.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdStructChecker_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdStructChecker.dir/structchecker.cpp.o -c /<>/Code/GraphMol/StructChecker/Wrap/structchecker.cpp [ 86%] Linking CXX executable testStructChecker cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/cmake -E cmake_link_script CMakeFiles/testStructChecker.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testStructChecker.dir/testStructChecker.cpp.o -o testStructChecker ../../../lib/libRDKitStructChecker.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 86%] Built target testStructChecker make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/RGroupDecomposition /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /<>/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= Scanning dependencies of target RGroupDecomposition make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 87%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp [ 87%] Linking CXX executable molHashCatchTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../../lib/libRDKitMolHash.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 87%] Built target molHashCatchTest make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= Scanning dependencies of target MolStandardize make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/MolStandardize.cpp [ 88%] Linking CXX shared module ../../../../rdkit/Chem/rdStructChecker.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdStructChecker.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdStructChecker.so CMakeFiles/rdStructChecker.dir/structchecker.cpp.o ../../../../lib/libRDKitStructChecker.so.1.2019.09.1 ../../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 88%] Built target rdStructChecker make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ChemReactions /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= Scanning dependencies of target testReaction make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 88%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/ChemReactions/testReaction.cpp [ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/PDBWriter.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:23, from /<>/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h:14, from /<>/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp:31: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/Metal.cpp [ 88%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2019.09.1 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o ../../../lib/libRDKitFMCS.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 In file included from /<>/Code/GraphMol/Wrap/PDBWriter.cpp:20: /<>/Code/RDBoost/python_streambuf.h: In constructor ‘boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)’: /<>/Code/RDBoost/python_streambuf.h:186:56: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h:156:58: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2019.09.1 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 88%] Built target RGroupDecomposition make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ChemReactions /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= Scanning dependencies of target testReactionFingerprints make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 88%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp /<>/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)’: /<>/Code/RDBoost/python_streambuf.h:379:16: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 379 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 88%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/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/CompressedSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 88%] Built target rdmolfiles make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ChemReactions /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= Scanning dependencies of target rxnTestCatch make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 88%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/ChemReactions/catch_tests.cpp [ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/Normalize.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/ChemReactions/testReaction.cpp:34: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/ChemReactions/testReaction.cpp:34: /usr/include/c++/9/bits/stl_vector.h: In member function ‘void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/ChemReactions/testReaction.cpp:34: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 88%] Linking CXX executable testReactionFingerprints cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 88%] Built target testReactionFingerprints make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ChemReactions /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --color= Scanning dependencies of target testEnumeration make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 89%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp [ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/Validate.cpp [ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/Charge.cpp [ 89%] Linking CXX executable testEnumeration cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 89%] 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 '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/ChemReactions/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= Scanning dependencies of target rdChemReactions make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 89%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/ChemReactions/catch_tests.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/ChemReactions/catch_tests.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/Tautomer.cpp [ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/Fragment.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/9/bits/stl_vector.h: In function ‘void boost::python::container_utils::extend_container(Container&, boost::python::api::object) [with Container = std::vector]’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In static member function ‘static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/9/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 184 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/9/bits/stl_vector.h: In static member function ‘static void boost::python::indexing_suite::base_delete_item(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]’: /usr/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ In file included from /usr/include/c++/9/algorithm:62, from /usr/include/boost/function/detail/prologue.hpp:13, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /<>/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/9/bits/stl_algo.h: In function ‘_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]’: /usr/include/c++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 112 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h: In static member function ‘static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]’: /usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 162 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 162 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 721 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/9/bits/stl_vector.h: In static member function ‘static void boost::python::vector_indexing_suite::base_extend(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]’: /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 1662 | _M_range_insert(__pos, __first, __last, | ^~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_vector.h: In static member function ‘static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]’: /usr/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/9/bits/vector.tcc:161:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | _M_realloc_insert(begin() + (__position - cbegin()), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/9/bits/vector.tcc:161:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | _M_realloc_insert(begin() + (__position - cbegin()), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 1662 | _M_range_insert(__pos, __first, __last, | ^~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 1662 | _M_range_insert(__pos, __first, __last, | ^~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/Code/RDBoost/Wrap.h:24, from /<>/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:689:9: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 689 | } | ^ /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:689:9: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:689:9: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:689:9: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp In file included from /usr/include/c++/9/vector:67, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/ChemReactions/testReaction.cpp:34: /usr/include/c++/9/bits/stl_vector.h: In function ‘void test25Conformers()’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ [ 90%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp [ 90%] Linking CXX executable rxnTestCatch cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 90%] Built target rxnTestCatch make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolDraw2D /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= Scanning dependencies of target MolDraw2D make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolDraw2D/MolDraw2D.cpp [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp /<>/Code/GraphMol/MolDraw2D/MolDraw2D.cpp: In member function ‘virtual void RDKit::MolDraw2D::drawBond(const RDKit::ROMol&, const RDKit::Bond*, int, int, const std::vector*, const std::map*, const std::vector*, const std::map*)’: /<>/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:1290:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1290 | if (at1_idx == bond->getBeginAtomIdx()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h:14, from /<>/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, T&) [with T = std::__cxx11::basic_string]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/QueryOps.h:19, from /<>/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:14: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/QueryOps.h:19, from /<>/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:14: /usr/include/c++/9/bits/stl_vector.h: In constructor ‘RDKit::Conformer::Conformer(unsigned int)’: /usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/QueryOps.h:19, from /<>/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:14: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/QueryOps.h:19, from /<>/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:14: /usr/include/c++/9/bits/stl_vector.h: In member function ‘void RDKit::MolDraw2D::extractAtomCoords(const RDKit::ROMol&, int, bool)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/set:60, from /<>/Code/Query/SetQuery.h:13, from /<>/Code/Query/QueryObjects.h:29, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/QueryOps.h:19, from /<>/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:14: /usr/include/c++/9/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2187:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2187 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Atom.h:26, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/QueryOps.h:19, from /<>/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:14: /usr/include/c++/9/bits/stl_map.h: In member function ‘RDKit::DrawColour RDKit::MolDraw2D::getColourByAtomicNum(int)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:67, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/QueryOps.h:19, from /<>/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:14: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void RDKit::MolDraw2D::drawReaction(const RDKit::ChemicalReaction&, bool, const std::vector*, const std::vector*)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/GraphMol/Atom.h:26, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/QueryOps.h:19, from /<>/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:14: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Geometry/point.h:16, from /<>/Code/GraphMol/MolPickler.h:14, from /<>/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:32: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h:14, from /<>/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void RDKit::Dict::setVal(const string&, T&) [with T = std::__cxx11::basic_string]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp [ 93%] Linking CXX executable testReaction cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Built target testReaction make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/RGroupDecomposition /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /<>/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake --color= Scanning dependencies of target testRGroupDecomp make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h:15, from /<>/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from /<>/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h:15, from /<>/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp:11: /usr/include/c++/9/bits/stl_vector.h: In function ‘void RDKit::MolDraw2D_detail::arcPoints(const RDGeom::Point2D&, const RDGeom::Point2D&, std::vector&, float, float)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp [ 93%] Linking CXX executable testRGroupDecomp cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2019.09.1 ../../../lib/libRDKitFMCS.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread [ 93%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Built target testRGroupDecomp make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/RGroupDecomposition/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake --color= Scanning dependencies of target rdRGroupDecomposition make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Built target rdChemReactions [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp [ 93%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2019.09.1 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2019.09.1 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Built target MolDraw2D make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolDraw2D /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= Scanning dependencies of target moldraw2DRxnTest1 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolDraw2D/rxn_test1.cpp [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h:14, from /<>/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘std::vector > RDKit::MolStandardize::readTransformations(std::istream&, int)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolDraw2D/rxn_test1.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:60, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolDraw2D/rxn_test1.cpp:12: /usr/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolDraw2D/rxn_test1.cpp:12: /usr/include/c++/9/bits/stl_map.h: In function ‘void {anonymous}::drawit(RDKit::ChemicalReaction*, std::string, bool, const std::vector*)’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolDraw2D /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= Scanning dependencies of target moldraw2DTestCatch make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolDraw2D/catch_tests.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h:14, from /<>/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp:10: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 [ 93%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2019.09.1 ../../../../lib/libRDKitFMCS.so.1.2019.09.1 ../../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Built target rdRGroupDecomposition make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolDraw2D /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= Scanning dependencies of target moldraw2DTest1 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolDraw2D/test1.cpp [ 93%] Linking CXX executable moldraw2DRxnTest1 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2019.09.1 ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Built target moldraw2DRxnTest1 make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolDraw2D/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolDraw2D make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 94%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp /usr/include/c++/9/bits/vector.tcc: In function ‘std::vector RDKit::MolStandardize::readTautomers(std::istream&, int)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 94%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2019.09.1 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.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2019.09.1 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 94%] Built target MolStandardize make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/Wrap /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= Scanning dependencies of target rdmolops make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/rdmolops.cpp /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp: In function ‘void RDKit::contourAndDrawGridHelper(RDKit::MolDraw2D&, boost::python::api::object&, boost::python::api::object&, boost::python::api::object&, unsigned int, boost::python::api::object&, const RDKit::MolDraw2DUtils::ContourParams&)’: /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:405:31: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 405 | if (PyArray_DIM(dataArr, 0) != xcoords->size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:411:31: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 411 | if (PyArray_DIM(dataArr, 1) != ycoords->size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolDraw2D/test1.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:60, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolDraw2D/test1.cpp:12: /usr/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolDraw2D/test1.cpp:12: /usr/include/c++/9/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In constructor ‘RDKit::MolDrawOptions::MolDrawOptions()’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/map:60, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolDraw2D/test1.cpp:12: /usr/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolDraw2D/test1.cpp:12: /usr/include/c++/9/bits/stl_map.h: In function ‘void test3()’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/Wrap/MolOps.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/RDGeneral/Dict.h:21, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolDraw2D/test1.cpp:12: /usr/include/c++/9/bits/vector.tcc: In function ‘void testGithub1322()’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /<>/Code/RDGeneral/Dict.h:19, from /<>/Code/RDGeneral/types.h:28, from /<>/Code/RDGeneral/utils.h:15, from /<>/Code/GraphMol/MolDraw2D/test1.cpp:12: /usr/include/c++/9/bits/stl_map.h: In function ‘void test14BWPalette()’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/Conformer.h:14, from /<>/Code/GraphMol/ROMol.h:36, from /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:17: /<>/Code/Geometry/point.h: In function ‘std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = RDGeom::Point2D]’: /<>/Code/Geometry/point.h:266:57: warning: ‘*((void*)(&)+16).RDGeom::Point2D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 266 | Point2D(const Point2D &other) : Point(other), x(other.x), y(other.y) {} | ~~~~~~^ /<>/Code/Geometry/point.h:266:69: warning: ‘*((void*)(&)+16).RDGeom::Point2D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 266 | Point2D(const Point2D &other) : Point(other), x(other.x), y(other.y) {} | ~~~~~~^ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:14: /<>/Code/RDBoost/Wrap.h: In function ‘std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = double]’: /<>/Code/RDBoost/Wrap.h:116:9: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 116 | T v = python::extract(obj[i]); | ^ In file included from /usr/include/c++/9/vector:67, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 96%] Linking CXX executable moldraw2DTest1 cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2019.09.1 ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread In file included from /usr/include/c++/9/map:60, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/Code/RDBoost/python.h:5, from /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: /usr/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/Code/RDBoost/python.h:5, from /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: /usr/include/c++/9/bits/stl_map.h: In function ‘void RDKit::useBWAtomPalette(RDKit::MolDrawOptions&)’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In function ‘void RDKit::{anonymous}::pyDictToColourMap(boost::python::api::object, RDKit::ColourPalette&)’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Built target moldraw2DTest1 make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= Scanning dependencies of target molStandardizeTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolStandardize/test1.cpp /usr/include/c++/9/bits/stl_map.h: In function ‘void RDKit::assignDefaultPalette(RDKit::ColourPalette&)’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/MolDraw2D/catch_tests.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/MolDraw2D/catch_tests.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp: In function ‘void RDKit::{anonymous}::pyDictToDoubleMap(boost::python::api::object, std::map&)’: /<>/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:72:57: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 72 | double r = python::extract(tDict.values()[i]); | ^ In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/MolDraw2D/catch_tests.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 96%] Linking CXX executable molStandardizeTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2019.09.1 ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Built target molStandardizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake --color= Scanning dependencies of target molStandardizeSmallTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolStandardize/test2.cpp In file included from /usr/include/c++/9/vector:72, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:44, from /usr/include/boost/lexical_cast.hpp:32, from /usr/include/boost/python/operators.hpp:19, from /usr/include/boost/python.hpp:49, from /<>/Code/RDBoost/python.h:3, from /<>/Code/GraphMol/Wrap/MolOps.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /<>/Code/GraphMol/Wrap/MolOps.cpp:30: /<>/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)’: /<>/Code/RDBoost/python_streambuf.h:379:16: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 379 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/Code/RDBoost/python_streambuf.h: In constructor ‘boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)’: /<>/Code/RDBoost/python_streambuf.h:186:56: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h:156:58: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ /<>/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekpos(boost_adaptbx::python::streambuf::pos_type, std::ios_base::openmode)’: /<>/Code/RDBoost/python_streambuf.h:379:16: warning: ‘*((void*)& +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 379 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:60, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/Code/RDBoost/python.h:5, from /<>/Code/GraphMol/Wrap/MolOps.cpp:12: /usr/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 96%] Linking CXX executable molStandardizeSmallTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2019.09.1 ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Built target molStandardizeSmallTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake --color= Scanning dependencies of target molValidateTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolStandardize/testValidate.cpp [ 96%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2019.09.1 ../../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Built target rdMolDraw2D make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= Scanning dependencies of target molNormalizeTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolStandardize/testNormalize.cpp In file included from /usr/include/c++/9/map:61, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/Code/RDBoost/python.h:5, from /<>/Code/GraphMol/Wrap/MolOps.cpp:12: /usr/include/c++/9/bits/stl_map.h: In function ‘std::string RDKit::molToSVG(const RDKit::ROMol&, unsigned int, unsigned int, boost::python::api::object, bool, unsigned int, unsigned int, bool, int)’: /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 96%] Linking CXX executable molNormalizeTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2019.09.1 ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Built target molNormalizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake --color= Scanning dependencies of target molChargeTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolStandardize/testCharge.cpp [ 96%] Linking CXX executable molValidateTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2019.09.1 ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Built target molValidateTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --color= Scanning dependencies of target molTautomerTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolStandardize/testTautomer.cpp [ 97%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E 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-I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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 /<>/Code/GraphMol/MolStandardize/testFragment.cpp [ 97%] Linking CXX executable moldraw2DTestCatch cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch 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/<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake --color= Scanning dependencies of target molStandardizeCatchTest make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 98%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/Wrap/Validate.cpp [100%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/Wrap/Charge.cpp [100%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp In file included from /usr/include/c++/9/vector:72, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/MolStandardize/catch_tests.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from /<>/External/catch/catch/single_include/catch.hpp:465, from /<>/Code/GraphMol/MolStandardize/catch_tests.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [100%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp [100%] Linking CXX executable molTautomerTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2019.09.1 ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [100%] Built target molTautomerTest [100%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_USE_BOOST_REGEX -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/<>/External/catch/catch/single_include -I/<>/External -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<>/Code -I/<>/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 /<>/Code/GraphMol/MolStandardize/Wrap/Metal.cpp [100%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -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 ../../../../lib/libRDKitMolStandardize.so.1.2019.09.1 ../../../../lib/libRDKitRDBoost.so.1.2019.09.1 -lpython3.8 /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../../lib/libRDKitCatalogs.so.1.2019.09.1 ../../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser ../../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [100%] Built target rdMolStandardize [100%] Linking CXX executable molStandardizeCatchTest cd /<>/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../../lib/libRDKitMolStandardize.so.1.2019.09.1 ../../../lib/libRDKitChemReactions.so.1.2019.09.1 ../../../lib/libRDKitChemTransforms.so.1.2019.09.1 ../../../lib/libRDKitDescriptors.so.1.2019.09.1 ../../../lib/libRDKitFileParsers.so.1.2019.09.1 ../../../lib/libRDKitPartialCharges.so.1.2019.09.1 ../../../lib/libRDKitDepictor.so.1.2019.09.1 ../../../lib/libRDKitMolAlign.so.1.2019.09.1 ../../../lib/libRDKitMolTransforms.so.1.2019.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2019.09.1 ../../../lib/libRDKitAlignment.so.1.2019.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2019.09.1 ../../../lib/libRDKitForceField.so.1.2019.09.1 ../../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../../lib/libRDKitTrajectory.so.1.2019.09.1 -lcoordgen -lmaeparser /usr/lib/arm-linux-gnueabihf/libboost_python38.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.71.0 /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.71.0 ../../../lib/libRDKitFilterCatalog.so.1.2019.09.1 ../../../lib/libRDKitCatalogs.so.1.2019.09.1 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.71.0 ../../../lib/libRDKitFingerprints.so.1.2019.09.1 ../../../lib/libRDKitSmilesParse.so.1.2019.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2019.09.1 ../../../lib/libRDKitSubgraphs.so.1.2019.09.1 ../../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [100%] Built target molStandardizeCatchTest make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles 0 make[2]: Leaving directory '/<>/obj-arm-linux-gnueabihf' STATIC_LINK=0 RDKIT_LIBDIR=/<>/obj-arm-linux-gnueabihf//lib pg_buildext build /<>/Code/PgSQL/rdkit build-%v ### build 12 ### make[2]: Entering directory '/<>/build-12' gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o rdkit_io.o /<>/Code/PgSQL/rdkit/rdkit_io.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o mol_op.o /<>/Code/PgSQL/rdkit/mol_op.c /<>/Code/PgSQL/rdkit/mol_op.c: In function ‘mol_murckoscaffold’: /<>/Code/PgSQL/rdkit/mol_op.c:263:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 263 | CROMol scaffold = MolMurckoScaffold(mol); | ^~~~~~ /<>/Code/PgSQL/rdkit/mol_op.c: In function ‘mol_hash’: /<>/Code/PgSQL/rdkit/mol_op.c:283:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 283 | char *res = pnstrdup(str, len); | ^~~~ /<>/Code/PgSQL/rdkit/mol_op.c: In function ‘mol_nm_hash’: /<>/Code/PgSQL/rdkit/mol_op.c:298:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 298 | char *str = computeNMMolHash(mol, opts); | ^~~~ /<>/Code/PgSQL/rdkit/mol_op.c:300:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 300 | char *res = pnstrdup(str, strlen(str)); | ^~~~ /<>/Code/PgSQL/rdkit/mol_op.c:293:7: warning: unused variable ‘len’ [-Wunused-variable] 293 | int len; | ^~~ /<>/Code/PgSQL/rdkit/mol_op.c: In function ‘mol_adjust_query_properties’: /<>/Code/PgSQL/rdkit/mol_op.c:313:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 313 | char *data = PG_GETARG_CSTRING(1); | ^~~~ /<>/Code/PgSQL/rdkit/mol_op.c:317:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 317 | Mol *res = deconstructROMol(adj); | ^~~ /<>/Code/PgSQL/rdkit/mol_op.c: In function ‘mol_to_svg’: /<>/Code/PgSQL/rdkit/mol_op.c:332:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 332 | char *legend = PG_GETARG_CSTRING(1); | ^~~~ /<>/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_smiles’: /<>/Code/PgSQL/rdkit/mol_op.c:356:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 356 | char *res = pnstrdup(str, strlen(str)); | ^~~~ In file included from /<>/Code/PgSQL/rdkit/mol_op.c:34: /<>/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_mol2s_transition’: /usr/include/postgresql/12/server/fmgr.h:263:29: warning: initialization of ‘CROMol’ {aka ‘void *’} from ‘Datum’ {aka ‘unsigned int’} makes pointer from integer without a cast [-Wint-conversion] 263 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value) | ^ /<>/Code/PgSQL/rdkit/mol_op.c:408:18: note: in expansion of macro ‘PG_GETARG_DATUM’ 408 | CROMol mol = PG_GETARG_DATUM(1); | ^~~~~~~~~~~~~~~ /<>/Code/PgSQL/rdkit/mol_op.c:424:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 424 | text *ts = (text *)palloc(ts_size); // new return value | ^~~~ In file included from /<>/Code/PgSQL/rdkit/mol_op.c:34: /usr/include/postgresql/12/server/fmgr.h:263:29: warning: initialization of ‘CROMol’ {aka ‘void *’} from ‘Datum’ {aka ‘unsigned int’} makes pointer from integer without a cast [-Wint-conversion] 263 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value) | ^ /<>/Code/PgSQL/rdkit/mol_op.c:436:18: note: in expansion of macro ‘PG_GETARG_DATUM’ 436 | CROMol mol = PG_GETARG_DATUM(1); | ^~~~~~~~~~~~~~~ /<>/Code/PgSQL/rdkit/mol_op.c:444:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 444 | char *smiles = makeMolText(mol, &len, false, false); | ^~~~ /<>/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_mols’: /<>/Code/PgSQL/rdkit/mol_op.c:482:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 482 | int32 ts_size = VARHDRSZ + strlen(str); | ^~~~~ In file included from /<>/Code/PgSQL/rdkit/mol_op.c:34: /<>/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_mol_transition’: /usr/include/postgresql/12/server/fmgr.h:263:29: warning: initialization of ‘CROMol’ {aka ‘void *’} from ‘Datum’ {aka ‘unsigned int’} makes pointer from integer without a cast [-Wint-conversion] 263 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value) | ^ /<>/Code/PgSQL/rdkit/mol_op.c:504:18: note: in expansion of macro ‘PG_GETARG_DATUM’ 504 | CROMol mol = PG_GETARG_DATUM(1); | ^~~~~~~~~~~~~~~ /usr/include/postgresql/12/server/fmgr.h:263:29: warning: initialization of ‘CROMol’ {aka ‘void *’} from ‘Datum’ {aka ‘unsigned int’} makes pointer from integer without a cast [-Wint-conversion] 263 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value) | ^ /<>/Code/PgSQL/rdkit/mol_op.c:515:18: note: in expansion of macro ‘PG_GETARG_DATUM’ 515 | CROMol mol = PG_GETARG_DATUM(1); | ^~~~~~~~~~~~~~~ /<>/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_smiles_transition’: /<>/Code/PgSQL/rdkit/mol_op.c:388:1: warning: control reaches end of non-void function [-Wreturn-type] 388 | } | ^ /<>/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_mol_transition’: /<>/Code/PgSQL/rdkit/mol_op.c:523:1: warning: control reaches end of non-void function [-Wreturn-type] 523 | } | ^ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o bfp_op.o /<>/Code/PgSQL/rdkit/bfp_op.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o sfp_op.o /<>/Code/PgSQL/rdkit/sfp_op.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o rxn_op.o /<>/Code/PgSQL/rdkit/rxn_op.c /<>/Code/PgSQL/rdkit/rxn_op.c:164:1: warning: multi-line comment [-Wcomment] 164 | // /* keep compiler quiet - no extra ; */ \ | ^ /<>/Code/PgSQL/rdkit/rxn_op.c: In function ‘reaction_to_svg’: /<>/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 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o rdkit_gist.o /<>/Code/PgSQL/rdkit/rdkit_gist.c /<>/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘soergeldistsign’: /<>/Code/PgSQL/rdkit/rdkit_gist.c:240:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 240 | uint8 *as = (uint8 *)VARDATA(a); | ^~~~~ /<>/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘soergeldist’: /<>/Code/PgSQL/rdkit/rdkit_gist.c:275:16: warning: implicit declaration of function ‘floor’ [-Wimplicit-function-declaration] 275 | return (int) floor(10000*soergeldistsign(a, b)); | ^~~~~ /<>/Code/PgSQL/rdkit/rdkit_gist.c:275:16: warning: incompatible implicit declaration of built-in function ‘floor’ /<>/Code/PgSQL/rdkit/rdkit_gist.c:42:1: note: include ‘’ or provide a declaration of ‘floor’ 41 | #include "bitstring.h" +++ |+#include 42 | /<>/Code/PgSQL/rdkit/rdkit_gist.c:262:10: warning: unused variable ‘d’ [-Wunused-variable] 262 | double d; | ^ /<>/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘gmol_consistent’: /<>/Code/PgSQL/rdkit/rdkit_gist.c:526:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 526 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /<>/Code/PgSQL/rdkit/rdkit_gist.c:538:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 538 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /<>/Code/PgSQL/rdkit/rdkit_gist.c:570:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 570 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /<>/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘rdkit_consistent’: /<>/Code/PgSQL/rdkit/rdkit_gist.c:658:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 658 | int siglen = SIGLEN(query); | ^~~ /<>/Code/PgSQL/rdkit/rdkit_gist.c:673:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 673 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /<>/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘gsfp_consistent’: /<>/Code/PgSQL/rdkit/rdkit_gist.c:708:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 708 | int sum, overlapSum, overlapN; | ^~~ /<>/Code/PgSQL/rdkit/rdkit_gist.c:714:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 714 | int nKey = (ISALLTRUE(key)) ? | ^~~ /<>/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘greaction_consistent’: /<>/Code/PgSQL/rdkit/rdkit_gist.c:787:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 787 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /<>/Code/PgSQL/rdkit/rdkit_gist.c:804:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 804 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /<>/Code/PgSQL/rdkit/rdkit_gist.c:832:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 832 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ At top level: /<>/Code/PgSQL/rdkit/rdkit_gist.c:646:1: warning: ‘rdkit_consistent’ defined but not used [-Wunused-function] 646 | rdkit_consistent(GISTENTRY *entry, StrategyNumber strategy, bytea *key, bytea *query) | ^~~~~~~~~~~~~~~~ /<>/Code/PgSQL/rdkit/rdkit_gist.c:261:1: warning: ‘soergeldist’ defined but not used [-Wunused-function] 261 | soergeldist(bytea *a, bytea *b) { | ^~~~~~~~~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o bfp_gist.o /<>/Code/PgSQL/rdkit/bfp_gist.c /<>/Code/PgSQL/rdkit/bfp_gist.c: In function ‘merge_key’: /<>/Code/PgSQL/rdkit/bfp_gist.c:699:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 699 | int siglen = GBFP_INNER_SIGLEN(result); | ^~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o bfp_gin.o /<>/Code/PgSQL/rdkit/bfp_gin.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o low_gist.o /<>/Code/PgSQL/rdkit/low_gist.c /<>/Code/PgSQL/rdkit/low_gist.c: In function ‘gslfp_consistent’: /<>/Code/PgSQL/rdkit/low_gist.c:410:30: warning: implicit declaration of function ‘searchSfpCache’ [-Wimplicit-function-declaration] 410 | fcinfo->flinfo->fn_extra = searchSfpCache( | ^~~~~~~~~~~~~~ /<>/Code/PgSQL/rdkit/low_gist.c:410:28: warning: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 410 | fcinfo->flinfo->fn_extra = searchSfpCache( | ^ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o guc.o /<>/Code/PgSQL/rdkit/guc.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o cache.o /<>/Code/PgSQL/rdkit/cache.c /<>/Code/PgSQL/rdkit/cache.c: In function ‘createCache’: /<>/Code/PgSQL/rdkit/cache.c:312:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 312 | methodsOrig = ctx->methods; | ^ In file included from /usr/include/postgresql/12/server/postgres.h:47, from /<>/Code/PgSQL/rdkit/cache.c:33: /<>/Code/PgSQL/rdkit/cache.c:341:19: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘unsigned int’ [-Wformat=] 341 | elog(ERROR, "Could not allocate %ld bytes", sizeof(*newholder)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~ | | | unsigned int /usr/include/postgresql/12/server/utils/elog.h:221:23: note: in definition of macro ‘elog’ 221 | elog_finish(elevel, __VA_ARGS__); \ | ^~~~~~~~~~~ /<>/Code/PgSQL/rdkit/cache.c:341:41: note: format string is defined here 341 | elog(ERROR, "Could not allocate %ld bytes", sizeof(*newholder)); | ~~^ | | | long int | %d g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o adapter.o /<>/Code/PgSQL/rdkit/adapter.cpp In file included from /usr/include/c++/9/vector:72, from /<>/Code/Query/Query.h:18, from /<>/Code/Query/QueryObjects.h:20, from /<>/Code/GraphMol/Atom.h:25, from /<>/Code/GraphMol/RDKitBase.h:23, from /<>/Code/PgSQL/rdkit/adapter.cpp:32: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o bitstring.o /<>/Code/PgSQL/rdkit/bitstring.c /<>/Code/PgSQL/rdkit/bitstring.c: In function ‘bitstringUnion’: /<>/Code/PgSQL/rdkit/bitstring.c:72:7: warning: unused variable ‘i’ [-Wunused-variable] 72 | int i; | ^ /<>/Code/PgSQL/rdkit/bitstring.c: In function ‘bitstringIntersection’: /<>/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 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -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/arm-linux-gnueabihf -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib/llvm-10/lib -L/usr/lib/arm-linux-gnueabihf/mit-krb5 -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -L/<>/obj-arm-linux-gnueabihf//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/' \ /<>/Code/PgSQL/rdkit/rdkit.sql.in > rdkit--3.8.sql /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o rdkit_io.bc /<>/Code/PgSQL/rdkit/rdkit_io.c /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o mol_op.bc /<>/Code/PgSQL/rdkit/mol_op.c /<>/Code/PgSQL/rdkit/mol_op.c:388:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ /<>/Code/PgSQL/rdkit/mol_op.c:408:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned int') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /<>/Code/PgSQL/rdkit/mol_op.c:436:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned int') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /<>/Code/PgSQL/rdkit/mol_op.c:504:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned int') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /<>/Code/PgSQL/rdkit/mol_op.c:515:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned int') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /<>/Code/PgSQL/rdkit/mol_op.c:523:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 6 warnings generated. /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o bfp_op.bc /<>/Code/PgSQL/rdkit/bfp_op.c /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o sfp_op.bc /<>/Code/PgSQL/rdkit/sfp_op.c /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o rxn_op.bc /<>/Code/PgSQL/rdkit/rxn_op.c /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o rdkit_gist.bc /<>/Code/PgSQL/rdkit/rdkit_gist.c /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o bfp_gist.bc /<>/Code/PgSQL/rdkit/bfp_gist.c /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o bfp_gin.bc /<>/Code/PgSQL/rdkit/bfp_gin.c /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o low_gist.bc /<>/Code/PgSQL/rdkit/low_gist.c /<>/Code/PgSQL/rdkit/low_gist.c:410:30: warning: implicit declaration of function 'searchSfpCache' is invalid in C99 [-Wimplicit-function-declaration] fcinfo->flinfo->fn_extra = searchSfpCache( ^ /<>/Code/PgSQL/rdkit/low_gist.c:410:28: warning: incompatible integer to pointer conversion assigning to 'void *' from 'int' [-Wint-conversion] fcinfo->flinfo->fn_extra = searchSfpCache( ^ ~~~~~~~~~~~~~~~ 2 warnings generated. /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o guc.bc /<>/Code/PgSQL/rdkit/guc.c /usr/bin/clang-10 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o cache.bc /<>/Code/PgSQL/rdkit/cache.c /<>/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-10 -xc++ -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/<>/Code -DRDKITVER='"007300"' -I. -I/<>/Code/PgSQL/rdkit -I/usr/include/postgresql/12/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -emit-llvm -c -o adapter.bc /<>/Code/PgSQL/rdkit/adapter.cpp In file included from /<>/Code/PgSQL/rdkit/adapter.cpp:54: /<>/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h:74:8: warning: 'tagAtoms' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] void tagAtoms(const ROMol &mol) { tagAtoms(mol, 0.2); } ^ /<>/Code/GraphMol/MolDraw2D/MolDraw2D.h:429:16: note: overridden virtual function is here virtual void tagAtoms(const ROMol &mol) { RDUNUSED_PARAM(mol); }; ^ 1 warning generated. opt-9 -module-summary -f adapter.bc -o adapter.bc make[2]: opt-9: Command not found make[2]: *** [/<>/Code/PgSQL/rdkit/Makefile:120: adapter.bc] Error 127 make[2]: *** Deleting file 'adapter.bc' make[2]: Leaving directory '/<>/build-12' make[1]: *** [debian/rules:89: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>' make: *** [debian/rules:36: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20200412-0956 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 2525352 Build-Time: 7352 Distribution: focal Fail-Stage: build Host Architecture: armhf Install-Time: 312 Job: rdkit_201909.1-2ubuntu5.dsc Machine Architecture: arm64 Package: rdkit Package-Time: 7681 Source-Version: 201909.1-2ubuntu5 Space: 2525352 Status: attempted Version: 201909.1-2ubuntu5 -------------------------------------------------------------------------------- Finished at 20200412-0956 Build needed 02:08:01, 2525352k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-18968999 Scanning for processes to kill in build PACKAGEBUILD-18968999