------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=5.9 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for rdkit-2020.09.3: DOCS=on: Build and/or install documentation PYTHON=on: Python bindings or support ===> Use 'make config' to modify these settings SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/construction/science/rdkit XDG_CONFIG_HOME=/construction/science/rdkit HOME=/construction/science/rdkit TMPDIR="/tmp" PATH=/construction/science/rdkit/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/science/rdkit XDG_CONFIG_HOME=/construction/science/rdkit HOME=/construction/science/rdkit TMPDIR="/tmp" PATH=/construction/science/rdkit/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/science/rdkit/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- SHLIB_VER=2020.09.3 PORTDOCS="" DOCS="" NO_DOCS="@comment " PYTHON="" NO_PYTHON="@comment " LITTLE_ENDIAN="" CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_EXT_SUFFIX= PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=5.9 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/RDKit" EXAMPLESDIR="share/examples/rdkit" DATADIR="share/RDKit" WWWDIR="www/rdkit" ETCDIR="etc/rdkit" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- DOCS="" NO_DOCS="@comment " PYTHON="" NO_PYTHON="@comment " PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/RDKit DOCSDIR=/usr/local/share/doc/RDKit EXAMPLESDIR=/usr/local/share/examples/rdkit WWWDIR=/usr/local/www/rdkit ETCDIR=/usr/local/etc/rdkit SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500906 OSVERSION=9999999 OSREL=5.9 _OSRELEASE=5.9-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/catch-2.13.3.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/flex-2.6.4_2.txz Installing /packages/All/rapidjson-1.1.0.524.txz Installing /packages/All/gmp-6.2.1.txz Installing /packages/All/mpfr-4.1.0.txz Installing /packages/All/metis-5.1.0_8.txz ===== Message from metis-5.1.0_8: -- ===> NOTICE: The metis port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Installing /packages/All/tbb-2020.3_1.txz Installing /packages/All/mpc-1.1.0_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/binutils-2.33.1_4,1.txz Installing /packages/All/gcc8-8.4.0.txz ===== Message from gcc8-8.4.0: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/openblas-0.3.12,1.txz Installing /packages/All/suitesparse-5.8.1.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/expat-2.2.10.txz Installing /packages/All/ncurses-6.2.20210116.txz Installing /packages/All/readline-8.0.4_1.txz Installing /packages/All/openssl-1.1.1i,1.txz Installing /packages/All/python37-3.7.9_1.txz ===== Message from python37-3.7.9_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/py37-setuptools-44.0.0.txz Installing /packages/All/py37-numpy-1.16.6,1.txz Installing /packages/All/libtextstyle-0.21.txz Installing /packages/All/m4-1.4.18_1,1.txz Installing /packages/All/bison-3.6.4,1.txz Installing /packages/All/libnghttp2-1.42.0.txz Installing /packages/All/ca_root_nss-3.58.txz ===== Message from ca_root_nss-3.58: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/curl-7.74.0.txz Installing /packages/All/libuv-1.40.0.txz Installing /packages/All/rhash-1.4.1.txz Installing /packages/All/liblz4-1.9.3,1.txz Installing /packages/All/libarchive-3.4.3_1,1.txz Installing /packages/All/cmake-3.19.2.txz Installing /packages/All/blas-3.5.0_6.txz Installing /packages/All/lapack-3.5.0_8.txz Installing /packages/All/superlu-5.2.2.txz Installing /packages/All/icu-68.2,1.txz Installing /packages/All/boost-libs-1.72.0_3.txz ===== Message from boost-libs-1.72.0_3: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. Installing /packages/All/adol-c-2.7.2.txz Installing /packages/All/fftw3-3.3.9.txz Installing /packages/All/libxml2-2.9.10_2.txz Installing /packages/All/wayland-1.18.0.txz Installing /packages/All/zstd-1.4.5_1.txz Installing /packages/All/pciids-20201127.txz Installing /packages/All/libpciaccess-0.16.txz Installing /packages/All/libdrm-2.4.101.txz Installing /packages/All/libunwind-20200331_1.txz Installing /packages/All/libpthread-stubs-0.4.txz Installing /packages/All/libXau-1.0.9.txz Installing /packages/All/xorgproto-2020.1.txz Installing /packages/All/libXdmcp-1.1.3.txz Installing /packages/All/libxcb-1.14_1.txz Installing /packages/All/libX11-1.6.12,1.txz Installing /packages/All/libXfixes-5.0.3_2.txz Installing /packages/All/libXdamage-1.1.5.txz Installing /packages/All/libXext-1.3.4,1.txz Installing /packages/All/libxshmfence-1.3.txz Installing /packages/All/libXxf86vm-1.1.4_3.txz Installing /packages/All/libXrender-0.9.10_2.txz Installing /packages/All/libXrandr-1.5.2.txz Installing /packages/All/mesa-libs-20.2.3.txz Installing /packages/All/eigen-3.3.8.txz Installing /packages/All/maeparser-1.2.4.txz Installing /packages/All/coordgenlibs-1.4.2.txz Installing /packages/All/png-1.6.37.txz Installing /packages/All/freetype2-2.10.4.txz ===== Message from freetype2-2.10.4: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/site/index.html, if documentation was installed). Installing /packages/All/py37-boost-libs-1.72.0_1.txz ===== Message from py37-boost-libs-1.72.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. Installing /packages/All/jbigkit-2.1_1.txz Installing /packages/All/jpeg-turbo-2.0.6.txz Installing /packages/All/tiff-4.2.0.txz Installing /packages/All/lcms2-2.11_1.txz Installing /packages/All/openjpeg-2.4.0.txz Installing /packages/All/giflib-5.2.1.txz Installing /packages/All/webp-1.1.0.txz Installing /packages/All/fontconfig-2.13.92_2,1.txz Running fc-cache to build fontconfig cache... Font directories: /usr/local/share/fonts /usr/local/lib/X11/fonts /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded Installing /packages/All/tcl86-8.6.11_1.txz Installing /packages/All/libXft-2.3.3.txz Installing /packages/All/libXScrnSaver-1.2.3_2.txz Installing /packages/All/tk86-8.6.11_2.txz Installing /packages/All/py37-olefile-0.46.txz Installing /packages/All/py37-tkinter-3.7.9_6.txz Installing /packages/All/py37-pillow-7.0.0.txz Installing /packages/All/qhull-7.2.1,1.txz Installing /packages/All/py37-six-1.15.0.txz Installing /packages/All/py37-cycler-0.10.0.txz Installing /packages/All/py37-dateutil-2.8.1.txz Installing /packages/All/py37-pytz-2020.5,1.txz Installing /packages/All/py37-pyparsing-2.4.7.txz Installing /packages/All/py37-tornado-5.1.1.txz Installing /packages/All/py37-zipp-3.4.0.txz Installing /packages/All/py37-typing-extensions-3.7.4.3.txz Installing /packages/All/py37-importlib-metadata-3.3.0_1.txz Installing /packages/All/py37-pluggy-0.13.1.txz Installing /packages/All/py37-certifi-2020.12.5.txz Installing /packages/All/py37-kiwisolver-1.1.0,1.txz Installing /packages/All/py37-matplotlib-3.3.3.txz Installing /packages/All/libfontenc-1.1.4.txz Installing /packages/All/mkfontscale-1.2.1.txz Installing /packages/All/adobe-cmaps-20051217_4.txz Installing /packages/All/py37-reportlab-3.5.57.txz UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:01:54 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> rdkit-2020.09.3 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> rdkit-2020.09.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by rdkit-2020.09.3 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> rdkit-2020.09.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by rdkit-2020.09.3 for building => SHA256 Checksum OK for rdkit-rdkit-Release_2020_09_3_GH0.tar.gz. => SHA256 Checksum OK for rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz. SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> rdkit-2020.09.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by rdkit-2020.09.3 for building ===> Extracting for rdkit-2020.09.3 => SHA256 Checksum OK for rdkit-rdkit-Release_2020_09_3_GH0.tar.gz. => SHA256 Checksum OK for rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz. Extracted Memory Use: 125.09M SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for rdkit-2020.09.3 ===> Applying ports patches for rdkit-2020.09.3 from /xports/science/rdkit/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> rdkit-2020.09.3 depends on package: catch>0 - found ===> rdkit-2020.09.3 depends on executable: flex - found ===> rdkit-2020.09.3 depends on package: rapidjson>=0 - found ===> rdkit-2020.09.3 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> rdkit-2020.09.3 depends on executable: bison - found ===> rdkit-2020.09.3 depends on file: /usr/local/bin/cmake - found ===> rdkit-2020.09.3 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> rdkit-2020.09.3 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> rdkit-2020.09.3 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so) ===> rdkit-2020.09.3 depends on shared library: libcoordgen.so - found (/usr/local/lib/libcoordgen.so) ===> rdkit-2020.09.3 depends on shared library: libfreetype.so - found (/usr/local/lib/libfreetype.so) ===> rdkit-2020.09.3 depends on shared library: libmaeparser.so - found (/usr/local/lib/libmaeparser.so) ===> rdkit-2020.09.3 depends on shared library: libboost_python37.so - found (/usr/local/lib/libboost_python37.so) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> rdkit-2020.09.3 depends on package: catch>0 - found ===> rdkit-2020.09.3 depends on executable: flex - found ===> rdkit-2020.09.3 depends on package: rapidjson>=0 - found ===> rdkit-2020.09.3 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> rdkit-2020.09.3 depends on executable: bison - found ===> rdkit-2020.09.3 depends on file: /usr/local/bin/cmake - found ===> rdkit-2020.09.3 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> rdkit-2020.09.3 depends on file: /usr/local/bin/python3.7 - found ===> rdkit-2020.09.3 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so) ===> rdkit-2020.09.3 depends on shared library: libcoordgen.so - found (/usr/local/lib/libcoordgen.so) ===> rdkit-2020.09.3 depends on shared library: libfreetype.so - found (/usr/local/lib/libfreetype.so) ===> rdkit-2020.09.3 depends on shared library: libmaeparser.so - found (/usr/local/lib/libmaeparser.so) ===> rdkit-2020.09.3 depends on shared library: libboost_python37.so - found (/usr/local/lib/libboost_python37.so) ===> Configuring for rdkit-2020.09.3 ===> Performing out-of-source build /bin/mkdir -p /construction/science/rdkit/.build -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Found Catch2: /usr/local/include/catch2 CATCH: /usr/local/include/catch2 -- Found PythonInterp: /usr/local/bin/python3.7 (found version "3.7.9") -- Found PythonLibs: /usr/local/lib/libpython3.7m.so (found version "3.7.9") CMake Warning at /usr/local/share/cmake/Modules/FindBoost.cmake:2039 (message): No header defined for python-py37; skipping header check (note: header-only libraries have no designated component) Call Stack (most recent call first): CMakeLists.txt:279 (find_package) Python Install directory /usr/local/lib/python3.7/site-packages PYTHON Py_ENABLE_SHARED: 1 PYTHON USING LINK LINE: -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -- Found Eigen3: /usr/local/include/eigen3 (Required is at least version "2.91.0") -- Looking for pthread.h -- Looking for pthread.h - found -- Found Threads: TRUE -- Found Boost: /usr/local/include (found suitable version "1.72.0", minimum required is "1.58.0") found components: serialization == Using strict rotor definition -- Found Boost: /usr/local/include (found suitable version "1.72.0", minimum required is "1.58.0") found components: system iostreams regex -- maeparser include dir set as '/usr/local/include' -- maeparser libraries set as '/usr/local/lib/libmaeparser.so' -- Found maeparser: /usr/local/include -- coordgen include dir set as /usr/local/include -- coordgen libraries set as '/usr/local/lib/libcoordgen.so' -- Found coordgen: /usr/local/include -- Found RingDecomposerLib source in /construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -- Found Boost: /usr/local/include (found suitable version "1.72.0", minimum required is "1.58.0") found components: iostreams regex -- Found Boost: /usr/local/include (found suitable version "1.72.0", minimum required is "1.58.0") found components: system iostreams regex -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") == Updating Filters.cpp from pains file == Done updating pains files -- Found Freetype: /usr/local/lib/libfreetype.so (found version "2.10.4") -- Found RapidJSON source in /construction/science/rdkit/rdkit-Release_2020_09_3/External -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG RDK_OPTIMIZE_NATIVE -- Build files have been written to: /construction/science/rdkit/.build SUCCEEDED 00:00:07 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for rdkit-2020.09.3 /usr/local/bin/cmake -S/construction/science/rdkit/rdkit-Release_2020_09_3 -B/construction/science/rdkit/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/science/rdkit/.build/CMakeFiles /construction/science/rdkit/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- External/catch/CMakeFiles/catch.dir/all --- --- External/INCHI-API/CMakeFiles/inchi_support.dir/all --- --- External/CoordGen/CMakeFiles/coordgen_support.dir/all --- --- External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/all --- /usr/bin/make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend --- External/catch/CMakeFiles/catch.dir/all --- /usr/bin/make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/depend --- External/INCHI-API/CMakeFiles/inchi_support.dir/all --- /usr/bin/make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend --- External/CoordGen/CMakeFiles/coordgen_support.dir/all --- /usr/bin/make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend --- External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/all --- --- External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend --- --- External/INCHI-API/CMakeFiles/inchi_support.dir/all --- --- External/INCHI-API/CMakeFiles/inchi_support.dir/depend --- --- External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies /construction/science/rdkit/.build /construction/science/rdkit/.build/External/RingFamilies /construction/science/rdkit/.build/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake --- External/INCHI-API/CMakeFiles/inchi_support.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/External/INCHI-API /construction/science/rdkit/.build /construction/science/rdkit/.build/External/INCHI-API /construction/science/rdkit/.build/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake --- External/CoordGen/CMakeFiles/coordgen_support.dir/all --- --- External/CoordGen/CMakeFiles/coordgen_support.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/External/CoordGen /construction/science/rdkit/.build /construction/science/rdkit/.build/External/CoordGen /construction/science/rdkit/.build/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake --- External/catch/CMakeFiles/catch.dir/all --- --- External/catch/CMakeFiles/catch.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/External/catch /construction/science/rdkit/.build /construction/science/rdkit/.build/External/catch /construction/science/rdkit/.build/External/catch/CMakeFiles/catch.dir/DependInfo.cmake --- External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/all --- Scanning dependencies of target ringdecomposerlib_support --- External/INCHI-API/CMakeFiles/inchi_support.dir/all --- Scanning dependencies of target inchi_support --- External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/all --- 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target catch /usr/bin/make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/build --- External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/all --- [ 0%] Built target ringdecomposerlib_support --- External/CoordGen/CMakeFiles/coordgen_support.dir/all --- [ 0%] Built target coordgen_support --- External/catch/CMakeFiles/catch.dir/all --- [ 0%] Built target catch --- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/all --- --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/all --- --- Code/RDStreams/CMakeFiles/RDStreams.dir/all --- --- Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/all --- --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/all --- /usr/bin/make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend --- Code/RDStreams/CMakeFiles/RDStreams.dir/all --- /usr/bin/make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/depend --- 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DRingDecomposerLib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib--- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLbitset.c.o --- cd /construction/science/rdkit/.build/External/RingFamilies && /usr/bin/cc -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_URFLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DRingDecomposerLib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib--- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLcycleFams.c.o --- cd /construction/science/rdkit/.build/External/RingFamilies && /usr/bin/cc -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_URFLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DRingDecomposerLib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib--- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLdimacs.c.o --- [ 1%] Building C object External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLdimacs.c.o --- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLgraph.c.o --- [ 1%] Building C object External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLgraph.c.o --- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLhandler.c.o --- [ 1%] Building C object External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLhandler.c.o --- 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-I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib--- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLinfo.c.o --- [ 1%] Building C object External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLinfo.c.o --- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLdimacs.c.o --- /src/RingDecomposerLib/RDLdimacs.c.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib/RDLdimacs.c --- 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DRingDecomposerLib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLinfo.c.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib/RDLinfo.c --- Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/all --- Scanning dependencies of target hc /usr/bin/make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build --- Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o --- [ 1%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o cd /construction/science/rdkit/.build/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dhc_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/hc.dir/hc.c.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ML/Cluster/Murtagh/hc.c --- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/all --- --- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLrelation.c.o --- [ 1%] Building C object External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLrelation.c.o cd /construction/science/rdkit/.build/External/RingFamilies && /usr/bin/cc -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_URFLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION 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-I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDStreams/streams.cpp --- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/all --- --- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLstack.c.o --- [ 2%] Building C object External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLstack.c.o cd /construction/science/rdkit/.build/External/RingFamilies && /usr/bin/cc -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_URFLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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-I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDGeneral/Invariant.cpp --- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/all --- --- External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLutility.c.o --- [ 2%] Building C object External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLutility.c.o cd /construction/science/rdkit/.build/External/RingFamilies && /usr/bin/cc -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_URFLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/hc.dir/hcdriver.c.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ML/Cluster/Murtagh/hcdriver.c --- lib/libRDKithc.so.1.2020.09.3 --- [ 3%] Linking C shared library ../../../../lib/libRDKithc.so cd /construction/science/rdkit/.build/Code/ML/Cluster/Murtagh && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -pipe -O2 -fno-strict-aliasing -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2020.09.3 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o -pthread cd /construction/science/rdkit/.build/Code/ML/Cluster/Murtagh && /usr/local/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2020.09.3 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-fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RDGeneral.dir--- Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o --- cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RDGeneral.dir--- Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o --- /RDLog.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDGeneral/RDLog.cpp --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o --- /LocaleSwitcher.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDGeneral/LocaleSwitcher.cpp --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o --- /utils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDGeneral/utils.cpp --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o --- cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDGeneral/types.cpp --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o --- [ 5%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDGeneral/versions.cpp --- Code/RDStreams/CMakeFiles/RDStreams.dir/all --- --- lib/libRDKitRDStreams.so.1.2020.09.3 --- [ 6%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /construction/science/rdkit/.build/Code/RDStreams && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2020.09.3 CMakeFiles/RDStreams.dir/streams.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib /usr/local/lib/libboost_iostreams.so -pthread /usr/local/lib/libboost_regex.so cd /construction/science/rdkit/.build/Code/RDStreams && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2020.09.3 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so [ 6%] Built target RDStreams --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/all --- --- lib/libRDKitRDGeneral.so.1.2020.09.3 --- [ 6%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2020.09.3 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl -pthread cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeneral.so.1.2020.09.3 ../../lib/libRDKitRDGeneral.so.1 ../../lib/libRDKitRDGeneral.so [ 6%] Built target RDGeneral --- Code/RDBoost/CMakeFiles/RDBoost.dir/all --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- --- Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/all --- --- Code/Catalogs/CMakeFiles/Catalogs.dir/all --- --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/all --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- /usr/bin/make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend --- Code/Catalogs/CMakeFiles/Catalogs.dir/all --- /usr/bin/make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend --- Code/RDBoost/CMakeFiles/RDBoost.dir/all --- /usr/bin/make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend --- Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/all --- /usr/bin/make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/all --- /usr/bin/make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend --- Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/all --- --- Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Numerics/EigenSolvers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/Numerics/EigenSolvers /construction/science/rdkit/.build/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --- Code/RDBoost/CMakeFiles/RDBoost.dir/all --- --- Code/RDBoost/CMakeFiles/RDBoost.dir/depend --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/depend --- --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/all --- --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend --- --- Code/RDBoost/CMakeFiles/RDBoost.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/RDBoost /construction/science/rdkit/.build/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/DataStructs /construction/science/rdkit/.build/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/SimDivPickers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/SimDivPickers /construction/science/rdkit/.build/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --- Code/Catalogs/CMakeFiles/Catalogs.dir/all --- --- Code/Catalogs/CMakeFiles/Catalogs.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Catalogs /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/Catalogs /construction/science/rdkit/.build/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --- Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/all --- Scanning dependencies of target EigenSolvers /usr/bin/make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/all --- Scanning dependencies of target SimDivPickers /usr/bin/make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build --- Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/all --- --- Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o --- [ 6%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o cd /construction/science/rdkit/.build/Code/Numerics/EigenSolvers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/all --- --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o --- --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o --- --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o --- --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o --- [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o --- [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o --- cd /construction/science/rdkit/.build/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSimDivPickers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/SimDivPickers/MaxMinPicker.cpp --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o --- cd /construction/science/rdkit/.build/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSimDivPickers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/SimDivPickers/HierarchicalClusterPicker.cpp --- Code/RDBoost/CMakeFiles/RDBoost.dir/all --- Scanning dependencies of target RDBoost --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/all --- --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o --- [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o cd /construction/science/rdkit/.build/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSimDivPickers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/SimDivPickers/DistPicker.cpp --- Code/RDBoost/CMakeFiles/RDBoost.dir/all --- /usr/bin/make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build --- Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o --- [ 7%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o cd /construction/science/rdkit/.build/Code/RDBoost && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/Wrap.cpp --- Code/Catalogs/CMakeFiles/Catalogs.dir/all --- Scanning dependencies of target Catalogs /usr/bin/make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build --- Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o --- --- Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o --- --- Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o --- --- Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o --- [ 7%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o --- Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o --- [ 7%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Catalogs/CatalogEntry.cpp --- Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o --- cd /construction/science/rdkit/.build/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Catalogs/Catalog.cpp --- Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o --- [ 8%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o cd /construction/science/rdkit/.build/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Catalogs/CatalogParams.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- Scanning dependencies of target DataStructs /usr/bin/make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build --- Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o --- [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o --- Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o --- [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o --- Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o --- cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++1--- Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o --- cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++1--- Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o --- 1 -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/BitVect.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o --- 1 -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/SparseBitVect.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o --- [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o --- Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o --- [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/Utils.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o --- cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/ExplicitBitVect.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o --- [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/base64.cpp --- Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/all --- --- lib/libRDKitEigenSolvers.so.1.2020.09.3 --- [ 8%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /construction/science/rdkit/.build/Code/Numerics/EigenSolvers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/Numerics/EigenSolvers && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so [ 8%] Built target EigenSolvers --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o --- [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/BitOps.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o --- [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o --- Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o --- [ 9%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o --- Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o --- cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/DiscreteValueVect.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o --- cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/DiscreteDistMat.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o --- [ 9%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/FPBReader.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o --- [ 9%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/MultiFPBReader.cpp --- Code/Catalogs/CMakeFiles/Catalogs.dir/all --- --- lib/libRDKitCatalogs.so.1.2020.09.3 --- [ 9%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /construction/science/rdkit/.build/Code/Catalogs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2020.09.3 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/Catalogs && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so [ 9%] Built target Catalogs --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/all --- --- lib/libRDKitSimDivPickers.so.1.2020.09.3 --- [ 9%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /construction/science/rdkit/.build/Code/SimDivPickers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2020.09.3 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKithc.so.1.2020.09.3 ../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/SimDivPickers && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2020.09.3 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so [ 9%] Built target SimDivPickers --- Code/RDBoost/CMakeFiles/RDBoost.dir/all --- --- lib/libRDKitRDBoost.so.1.2020.09.3 --- [ 9%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /construction/science/rdkit/.build/Code/RDBoost && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2020.09.3 CMakeFiles/RDBoost.dir/Wrap.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so cd /construction/science/rdkit/.build/Code/RDBoost && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so [ 9%] Built target RDBoost --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- --- Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/all --- --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- /usr/bin/make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend --- Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/all --- /usr/bin/make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend --- Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ML/Cluster/Murtagh /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/ML/Cluster/Murtagh /construction/science/rdkit/.build/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/RDBoost/Wrap /construction/science/rdkit/.build/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake Scanning dependencies of target rdBase /usr/bin/make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build --- Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/all --- Scanning dependencies of target Clustering /usr/bin/make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o --- --- Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/all --- --- Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o --- --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- [ 9%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /construction/science/rdkit/.build/Code/RDBoost/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdBase_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/Wrap/RDBase.cpp --- Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/all --- [ 9%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o cd /construction/science/rdkit/.build/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ML/Cluster/Murtagh/Clustering.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- --- lib/libRDKitDataStructs.so.1.2020.09.3 --- [ 9%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /construction/science/rdkit/.build/Code/DataStructs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2020.09.3 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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/DataStructs && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so [ 9%] Built target DataStructs --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- --- Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/all --- --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all --- --- Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- /usr/bin/make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- /usr/bin/make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend --- Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/all --- /usr/bin/make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all --- /usr/bin/make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend --- Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/all --- /usr/bin/make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend --- --- Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/all --- --- Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend --- --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all --- --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend --- --- Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ML/InfoTheory /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/ML/InfoTheory /construction/science/rdkit/.build/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --- Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/all --- --- Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/DataStructs/Wrap /construction/science/rdkit/.build/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/SimDivPickers/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/SimDivPickers/Wrap /construction/science/rdkit/.build/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend --- --- Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataManip/MetricMatrixCalc/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/DataManip/MetricMatrixCalc/Wrap /construction/science/rdkit/.build/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/Geometry /construction/science/rdkit/.build/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --- Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/all --- Scanning dependencies of target InfoTheory /usr/bin/make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build --- Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o --- [ 9%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /construction/science/rdkit/.build/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ML/InfoTheory/InfoBitRanker.cpp --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- Scanning dependencies of target RDGeometryLib /usr/bin/make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all --- Scanning dependencies of target rdSimDivPickers /usr/bin/make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build --- Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/all --- Scanning dependencies of target rdMetricMatrixCalc /usr/bin/make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o --- --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o --- --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o --- --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o --- --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o --- [ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o --- [ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o --- [ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o --- cd /construction/science/rdkit/.build/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RDGeom--- Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o --- cd /construction/science/rdkit/.build/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RDGeom--- Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o --- cd /construction/science/rdkit/.build/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RDGeom--- Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o --- etryLib.dir/Transform2D.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/Transform2D.cpp --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o --- etryLib.dir/Transform3D.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/Transform3D.cpp --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o --- etryLib.dir/UniformGrid3D.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/UniformGrid3D.cpp --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all --- --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o --- --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o --- [ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o cd /construction/science/rdkit/.build/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.cpp --- 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-I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all --- [ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /construction/science/rdkit/.build/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdSimDivPickers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- Scanning dependencies of target cDataStructs /usr/bin/make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o --- [ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/Wrap/DataStructs.cpp --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/Wrap/RDBase.cpp:14: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII) { ~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if ((!df_isTextMode || c <= STD_ASCII) && ~~^~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII && ~~^~~~~~~~~~~ --- Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/all --- --- lib/libRDKitInfoTheory.so.1.2020.09.3 --- [ 11%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /construction/science/rdkit/.build/Code/ML/InfoTheory && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2020.09.3 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/ML/InfoTheory && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2020.09.3 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so [ 11%] Built target InfoTheory --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/all --- /usr/bin/make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ML/InfoTheory/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/ML/InfoTheory/Wrap /construction/science/rdkit/.build/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake Scanning dependencies of target rdInfoTheory /usr/bin/make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o --- [ 11%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o cd /construction/science/rdkit/.build/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdInfoTheory_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c 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-I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/GridUtils.cpp --- Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/all --- --- rdkit/ML/Cluster/Clustering.so --- --- Code/ML/Data/CMakeFiles/cQuantize.dir/all --- /usr/bin/make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend --- Code/ML/Data/CMakeFiles/cQuantize.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ML/Data /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/ML/Data /construction/science/rdkit/.build/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --- Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/all --- [ 11%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /construction/science/rdkit/.build/Code/ML/Cluster/Murtagh && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKithc.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so -pthread [ 12%] Built target Clustering --- Code/ML/Data/CMakeFiles/cQuantize.dir/all --- Scanning dependencies of target cQuantize /usr/bin/make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build --- Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o --- [ 12%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /construction/science/rdkit/.build/Code/ML/Data && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DcQuantize_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ML/Data/cQuantize.cpp --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all --- --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o --- --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o --- --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o --- --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o --- [ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o --- [ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o --- cd /construction/science/rdkit/.build/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdSimDivPickers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/SimDivPickers/Wrap/LeaderPicker.cpp --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o --- [ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o --- cd /construction/science/rdkit/.build/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdSimDivPickers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o --- cd /construction/science/rdkit/.build/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdSimDivPickers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o --- [ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/Wrap/DiscreteValueVect.cpp --- Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/all --- --- rdkit/DataManip/Metric/rdMetricMatrixCalc.so --- [ 13%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /construction/science/rdkit/.build/Code/DataManip/MetricMatrixCalc/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 13%] Built target rdMetricMatrixCalc --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o --- [ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/Wrap/SparseIntVect.cpp --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- --- lib/libRDKitRDGeometryLib.so.1.2020.09.3 --- [ 13%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /construction/science/rdkit/.build/Code/Geometry && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/Geometry && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so [ 13%] Built target RDGeometryLib --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/all --- /usr/bin/make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/Geometry/Wrap /construction/science/rdkit/.build/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake Scanning dependencies of target rdGeometry /usr/bin/make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o --- [ 13%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /construction/science/rdkit/.build/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdGeometry_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/Wrap/Point.cpp --- Code/Numerics/Alignment/CMakeFiles/Alignment.dir/all --- /usr/bin/make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend --- Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Numerics/Alignment /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/Numerics/Alignment /construction/science/rdkit/.build/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake Scanning dependencies of target Alignment /usr/bin/make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build --- Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o --- [ 13%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o cd /construction/science/rdkit/.build/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Numerics/Alignment/AlignPoints.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o --- [ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/Wrap/wrap_SparseBV.cpp --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/all --- --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o --- --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o --- --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o --- [ 14%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o cd /construction/science/rdkit/.build/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdInfoTheory_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o --- [ 14%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o cd /construction/science/rdkit/.build/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdInfoTheory_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp --- Code/Numerics/Alignment/CMakeFiles/Alignment.dir/all --- --- lib/libRDKitAlignment.so.1.2020.09.3 --- [ 14%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /construction/science/rdkit/.build/Code/Numerics/Alignment && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2020.09.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/Numerics/Alignment && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so [ 15%] Built target Alignment --- Code/GraphMol/CMakeFiles/GraphMol.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend --- Code/GraphMol/CMakeFiles/GraphMol.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --- Code/ML/Data/CMakeFiles/cQuantize.dir/all --- --- rdkit/ML/Data/cQuantize.so --- [ 15%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so cd /construction/science/rdkit/.build/Code/ML/Data && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitInfoTheory.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so -pthread [ 15%] Built target cQuantize --- Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/all --- /usr/bin/make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend --- Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ChemicalFeatures /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/ChemicalFeatures /construction/science/rdkit/.build/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake Scanning dependencies of target ChemicalFeatures /usr/bin/make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build --- Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o --- [ 15%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /construction/science/rdkit/.build/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ChemicalFeatures/FreeChemicalFeature.cpp --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all --- --- rdkit/SimDivFilters/rdSimDivPickers.so --- [ 15%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /construction/science/rdkit/.build/Code/SimDivPickers/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o --- --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all --- /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitSimDivPickers.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../lib/libRDKithc.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- [ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all --- [ 15%] Built target rdSimDivPickers --- Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/all --- /usr/bin/make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend --- Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Numerics/Alignment/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/Numerics/Alignment/Wrap /construction/science/rdkit/.build/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake Scanning dependencies of target rdAlignment /usr/bin/make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build --- Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o --- [ 15%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /construction/science/rdkit/.build/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdAlignment_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/all --- Scanning dependencies of target GraphMol /usr/bin/make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build --- Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o --- [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Atom.cpp --- Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/all --- --- lib/libRDKitChemicalFeatures.so.1.2020.09.3 --- [ 16%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /construction/science/rdkit/.build/Code/ChemicalFeatures && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2020.09.3 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/ChemicalFeatures && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2020.09.3 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so [ 16%] Built target ChemicalFeatures --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/all --- --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o --- [ 16%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o cd /construction/science/rdkit/.build/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdGeometry_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/Wrap/UniformGrid3D.cpp --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/all --- --- rdkit/ML/InfoTheory/rdInfoTheory.so --- [ 16%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so cd /construction/science/rdkit/.build/Code/ML/InfoTheory/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitInfoTheory.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 16%] Built target rdInfoTheory --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/all --- --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o --- [ 16%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o cd /construction/science/rdkit/.build/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdGeometry_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/Wrap/rdGeometry.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o --- [ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/Wrap/wrap_BitOps.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o --- [ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/Wrap/wrap_FPB.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o --- [ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DataStructs/Wrap/wrap_Utils.cpp --- Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/all --- --- rdkit/Numerics/rdAlignment.so --- [ 16%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /construction/science/rdkit/.build/Code/Numerics/Alignment/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 17%] Built target rdAlignment --- Code/GraphMol/CMakeFiles/GraphMol.dir/all --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o --- [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/QueryAtom.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o --- [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/QueryBond.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o --- [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Bond.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o --- [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolOps.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o --- [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FindRings.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o --- [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ROMol.cpp --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/all --- --- rdkit/Geometry/rdGeometry.so --- [ 18%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /construction/science/rdkit/.build/Code/Geometry/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 19%] Built target rdGeometry --- Code/GraphMol/CMakeFiles/GraphMol.dir/all --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o --- [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/RWMol.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o --- [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/PeriodicTable.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o --- [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/atomic_data.cpp --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- --- rdkit/rdBase.so --- [ 19%] Linking CXX shared module ../../../rdkit/rdBase.so cd /construction/science/rdkit/.build/Code/RDBoost/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so -pthread [ 19%] Built target rdBase --- Code/GraphMol/CMakeFiles/GraphMol.dir/all --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o --- [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/QueryOps.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o --- [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolPickler.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o --- [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Canon.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o --- [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD 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-mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/BondIterators.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- rdkit/DataStructs/cDataStructs.so --- [ 20%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 21%] Built target cDataStructs --- Code/GraphMol/CMakeFiles/GraphMol.dir/all --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o --- [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o --- Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o --- [ 21%] Building CXX 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-I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/AddHs.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o --- [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Matrices.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o --- [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD 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-I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Conformer.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o --- [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Renumber.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o --- [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/AdjustQuery.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o --- [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Resonance.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o --- [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/StereoGroup.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o --- [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/new_canon.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o --- [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SubstanceGroup.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o --- [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FindStereo.cpp --- lib/libRDKitGraphMol.so.1.2020.09.3 --- [ 24%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2020.09.3 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl -pthread cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so [ 24%] Built target GraphMol --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/all --- --- Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/all --- --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/all --- --- Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/all --- --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/all --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- --- Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/all --- --- Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/all --- --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- /usr/bin/make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/all --- /usr/bin/make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend --- Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/all --- /usr/bin/make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend --- Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/all --- /usr/bin/make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all --- /usr/bin/make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/all --- --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend --- --- Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/all --- --- Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend --- --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/PartialCharges /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/PartialCharges /construction/science/rdkit/.build/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --- Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolInterchange /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolInterchange /construction/science/rdkit/.build/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/all --- --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend --- --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all --- --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend --- --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolCatalog /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolCatalog /construction/science/rdkit/.build/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix 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/construction/science/rdkit/.build/Code/GraphMol/SmilesParse /construction/science/rdkit/.build/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --- Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/all --- --- Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolTransforms /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolTransforms /construction/science/rdkit/.build/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake --- Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Subgraphs /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Subgraphs /construction/science/rdkit/.build/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --- Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/all --- --- Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend --- --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/all --- --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend --- --- Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Trajectory /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Trajectory /construction/science/rdkit/.build/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Substruct /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Substruct /construction/science/rdkit/.build/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --- Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/all --- Scanning dependencies of target MolInterchange /usr/bin/make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build --- Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o --- [ 24%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/rapidjson-1.1.0/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolInterchange/Parser.cpp --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/all --- Scanning dependencies of target PartialCharges /usr/bin/make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o --- [ 24%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/PartialCharges/GasteigerCharges.cpp --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/all --- Scanning dependencies of target SubstructMatch /usr/bin/make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o --- --- Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/all --- Scanning dependencies of target MolTransforms 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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSubstructMatch_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Substruct/SubstructMatch.cpp --- Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/all --- --- Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o --- --- Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/all --- --- Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o --- [ 26%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DTrajectory_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Trajectory/Trajectory.cpp --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/all --- --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o --- [ 26%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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/construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp --- Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/all --- [ 26%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolTransforms/MolTransforms.cpp --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all --- Scanning dependencies of target SLNParse /usr/bin/make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o --- [ 26%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSLNParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SLNParse/SLNParse.cpp --- 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSubgraphs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Subgraphs/Subgraphs.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- 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/usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SmilesParse/SmilesParse.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- Scanning dependencies of target CIPLabeler /usr/bin/make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o --- [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/CIPMol.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o --- [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/all --- --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o --- [ 27%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/PartialCharges/GasteigerParams.cpp --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/all --- --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o --- [ 27%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolCatalog/MolCatalogParams.cpp --- Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/all --- --- Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o --- [ 27%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSubgraphs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Subgraphs/SubgraphUtils.cpp --- Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/all --- --- lib/libRDKitTrajectory.so.1.2020.09.3 --- [ 27%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /construction/science/rdkit/.build/Code/GraphMol/Trajectory && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2020.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Trajectory && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2020.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so [ 27%] Built target Trajectory --- Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/all --- /usr/bin/make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend --- Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Wrap /construction/science/rdkit/.build/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake Scanning dependencies of target rdqueries /usr/bin/make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build --- Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o --- [ 27%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdqueries_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/rdqueries.cpp --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/all --- --- lib/libRDKitMolCatalog.so.1.2020.09.3 --- [ 28%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /construction/science/rdkit/.build/Code/GraphMol/MolCatalog && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2020.09.3 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/MolCatalog && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2020.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so [ 28%] Built target MolCatalog --- Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/all --- /usr/bin/make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend --- Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ChemicalFeatures/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/ChemicalFeatures/Wrap /construction/science/rdkit/.build/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake Scanning dependencies of target rdChemicalFeatures /usr/bin/make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build --- Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o --- [ 28%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o cd /construction/science/rdkit/.build/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdChemicalFeatures_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o --- [ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp --- Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/all --- --- Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o --- [ 28%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/rapidjson-1.1.0/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolInterchange/Writer.cpp --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/all --- --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o --- [ 28%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSubstructMatch_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Substruct/SubstructUtils.cpp --- Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/all --- --- lib/libRDKitMolTransforms.so.1.2020.09.3 --- [ 28%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /construction/science/rdkit/.build/Code/GraphMol/MolTransforms && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/MolTransforms && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so [ 29%] Built target MolTransforms --- Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/all --- /usr/bin/make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend --- Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Numerics/Optimizer /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/Numerics/Optimizer /construction/science/rdkit/.build/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake Scanning dependencies of target Optimizer /usr/bin/make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build --- Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o --- [ 29%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /construction/science/rdkit/.build/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Numerics/Optimizer/BFGSOpt.cpp --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/all --- --- lib/libRDKitPartialCharges.so.1.2020.09.3 --- [ 29%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd /construction/science/rdkit/.build/Code/GraphMol/PartialCharges && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2020.09.3 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/PartialCharges && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so [ 29%] Built target PartialCharges --- Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/all --- /usr/bin/make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend --- Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Wrap /construction/science/rdkit/.build/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake Scanning dependencies of target rdtrajectory /usr/bin/make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build --- Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o --- [ 29%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdtrajectory_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/Trajectory.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o --- [ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/Mancude.cpp --- Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/all --- --- Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o --- [ 29%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /construction/science/rdkit/.build/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Numerics/Optimizer/LinearSearch.cpp --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all --- --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o --- [ 29%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSLNParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SLNParse/SLNAttribs.cpp --- Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/all --- --- Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o --- [ 30%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /construction/science/rdkit/.build/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdChemicalFeatures_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp --- Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/all --- --- lib/libRDKitSubgraphs.so.1.2020.09.3 --- [ 31%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /construction/science/rdkit/.build/Code/GraphMol/Subgraphs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Subgraphs && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so [ 31%] Built target Subgraphs --- Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/all --- /usr/bin/make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend --- Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolCatalog/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolCatalog/Wrap /construction/science/rdkit/.build/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake Scanning dependencies of target rdMolCatalog /usr/bin/make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build --- Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o --- [ 31%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolCatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o --- [ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SmilesParse/SmilesWrite.cpp --- Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/all --- --- lib/libRDKitOptimizer.so.1.2020.09.3 --- [ 32%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /construction/science/rdkit/.build/Code/Numerics/Optimizer && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2020.09.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitTrajectory.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread cd /construction/science/rdkit/.build/Code/Numerics/Optimizer && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2020.09.3 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so [ 32%] Built target Optimizer --- Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/all --- /usr/bin/make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend --- Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolTransforms/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolTransforms/Wrap /construction/science/rdkit/.build/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake Scanning dependencies of target rdMolTransforms /usr/bin/make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build --- Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o --- [ 32%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolTransforms_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o --- [ 33%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdqueries_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/Queries.cpp --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/all --- --- lib/libRDKitSubstructMatch.so.1.2020.09.3 --- [ 33%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /construction/science/rdkit/.build/Code/GraphMol/Substruct && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Substruct && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so [ 33%] Built target SubstructMatch --- Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/all --- /usr/bin/make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend --- Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ShapeHelpers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake Scanning dependencies of target ShapeHelpers /usr/bin/make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build --- Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o --- [ 33%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DShapeHelpers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp --- Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/all --- --- lib/libRDKitMolInterchange.so.1.2020.09.3 --- [ 34%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so cd /construction/science/rdkit/.build/Code/GraphMol/MolInterchange && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2020.09.3 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MolInterchange && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2020.09.3 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so [ 34%] Built target MolInterchange --- Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/all --- /usr/bin/make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend --- Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/PartialCharges/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/PartialCharges/Wrap /construction/science/rdkit/.build/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o --- [ 34%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/Digraph.cpp --- Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/all --- Scanning dependencies of target rdPartialCharges /usr/bin/make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build --- Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o --- [ 34%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdPartialCharges_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o --- [ 34%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdtrajectory_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/rdTrajectory.cpp --- Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/all --- --- Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o --- [ 34%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DShapeHelpers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp --- Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/all --- --- rdkit/Chem/rdChemicalFeatures.so --- [ 34%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so cd /construction/science/rdkit/.build/Code/ChemicalFeatures/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitChemicalFeatures.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 34%] Built target rdChemicalFeatures --- Code/ForceField/CMakeFiles/ForceField.dir/all --- /usr/bin/make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend --- Code/ForceField/CMakeFiles/ForceField.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/ForceField /construction/science/rdkit/.build/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake Scanning dependencies of target ForceField /usr/bin/make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build --- Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o --- [ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/ForceField.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o --- [ 34%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/Node.cpp --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all --- --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o --- [ 34%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSLNParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SLNParse/sln.tab.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o --- [ 34%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SmilesParse/SmartsWrite.cpp --- Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/all --- --- rdkit/Chem/rdPartialCharges.so --- [ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /construction/science/rdkit/.build/Code/GraphMol/PartialCharges/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 34%] Built target rdPartialCharges --- Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/all --- /usr/bin/make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend --- Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolAlign /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolAlign /construction/science/rdkit/.build/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake Scanning dependencies of target MolAlign /usr/bin/make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build --- Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o --- [ 34%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolAlign/AlignMolecules.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o --- [ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/UFF/AngleBend.cpp --- Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/all --- --- rdkit/Chem/rdMolTransforms.so --- [ 35%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /construction/science/rdkit/.build/Code/GraphMol/MolTransforms/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 35%] Built target rdMolTransforms --- Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/all --- /usr/bin/make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend --- Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolInterchange/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolInterchange/Wrap /construction/science/rdkit/.build/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o --- [ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/Edge.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/all --- --- rdkit/Chem/rdtrajectory.so --- [ 36%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitTrajectory.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so -pthread [ 37%] Built target rdtrajectory --- Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/all --- Scanning dependencies of target rdMolInterchange /usr/bin/make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build --- Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o --- [ 37%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolInterchange_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/rapidjson-1.1.0/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp --- Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/all --- --- lib/libRDKitShapeHelpers.so.1.2020.09.3 --- [ 37%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2020.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2020.09.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so [ 38%] Built target ShapeHelpers --- Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/all --- /usr/bin/make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend --- Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ShapeHelpers/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers/Wrap /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake Scanning dependencies of target rdShapeHelpers /usr/bin/make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build --- Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o --- [ 39%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdShapeHelpers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all --- --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o --- [ 39%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSLNParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SLNParse/lex.yysln.cpp --- Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/all --- --- rdkit/Chem/rdMolCatalog.so --- [ 40%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so cd /construction/science/rdkit/.build/Code/GraphMol/MolCatalog/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitMolCatalog.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../../lib/libRDKitCatalogs.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 40%] Built target rdMolCatalog --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o --- [ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/Sort.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o --- [ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o --- [ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o --- [ 40%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS 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/construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/UFF/BondStretch.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o --- [ 40%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/UFF/Nonbonded.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o --- [ 40%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o --- [ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all --- --- lib/libRDKitSLNParse.so.1.2020.09.3 --- [ 40%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2020.09.3 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2020.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so [ 40%] Built target SLNParse --- Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/all --- /usr/bin/make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend --- Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SLNParse/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/SLNParse/Wrap /construction/science/rdkit/.build/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o --- [ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp --- Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/all --- Scanning dependencies of target rdSLNParse /usr/bin/make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build --- Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o --- [ 41%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdSLNParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp --- Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/all --- --- lib/libRDKitMolAlign.so.1.2020.09.3 --- [ 41%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2020.09.3 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so [ 41%] Built target MolAlign --- External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/all --- /usr/bin/make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend --- External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/External/CoordGen/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/External/CoordGen/Wrap /construction/science/rdkit/.build/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o --- [ 42%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp --- Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/all --- --- rdkit/Chem/rdMolInterchange.so --- [ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so cd 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../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 42%] Built target rdMolInterchange --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/all --- /usr/bin/make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Depictor /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Depictor /construction/science/rdkit/.build/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --- Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/all --- --- rdkit/Chem/rdqueries.so --- [ 42%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 42%] Built target rdqueries --- External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/all --- Scanning dependencies of target rdCoordGen /usr/bin/make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/all --- Scanning dependencies of target Depictor /usr/bin/make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build --- External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/all --- --- External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o --- [ 42%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o cd /construction/science/rdkit/.build/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdCoordGen_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/External/CoordGen/Wrap/rdCoordGen.cpp --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/all --- --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o --- --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o --- --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o --- [ 43%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o --- [ 43%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o --- cd /construction/science/rdkit/.build/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Depictor/RDDepictor.cpp --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o --- cd /construction/science/rdkit/.build/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Depictor/EmbeddedFrag.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o --- [ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o --- [ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/UFF/Inversion.cpp --- Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/all --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Conformer.h:14, from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ROMol.h:36, from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:13: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h: In function 'boost::python::tuple RDKit::getUnionOfTwoBox(boost::python::tuple, boost::python::tuple)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:31: warning: '*((void*)(&)+32).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:43: warning: '*((void*)(&)+32).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:55: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:31: warning: '*((void*)(&)+32).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:43: warning: '*((void*)(&)+32).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:55: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:31: warning: '*((void*)(&)+32).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:43: warning: '*((void*)(&)+32).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:55: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:31: warning: '*((void*)(&)+32).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:43: warning: '*((void*)(&)+32).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:55: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o --- [ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o --- [ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp --- Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/all --- --- rdkit/Chem/rdShapeHelpers.so --- [ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitShapeHelpers.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 43%] Built target rdShapeHelpers --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o --- --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o --- [ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o --- [ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o --- [ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o --- [ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o --- [ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o --- [ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o --- [ 44%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/UFF/TorsionAngle.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o --- [ 44%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SmilesParse/smarts.tab.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o --- [ 44%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/UFF/DistanceConstraint.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o --- [ 44%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SmilesParse/smiles.tab.cpp --- Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/all --- --- rdkit/Chem/rdSLNParse.so --- [ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitSLNParse.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 44%] Built target rdSLNParse --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o --- [ 45%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/UFF/AngleConstraint.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o --- [ 45%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/UFF/TorsionConstraint.cpp --- Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/all --- --- lib/libRDKitCIPLabeler.so.1.2020.09.3 --- [ 45%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2020.09.3 CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o CMakeFiles/CIPLabeler.dir/Node.cpp.o CMakeFiles/CIPLabeler.dir/Edge.cpp.o CMakeFiles/CIPLabeler.dir/Sort.cpp.o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2020.09.3 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so [ 45%] Built target CIPLabeler --- Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/all --- /usr/bin/make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend --- Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler/Wrap /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake Scanning dependencies of target rdCIPLabeler /usr/bin/make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build --- Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o --- [ 45%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdCIPLabeler_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/all --- --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o --- [ 45%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Depictor/DepictUtils.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o --- [ 45%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/UFF/PositionConstraint.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o --- [ 46%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SmilesParse/lex.yysmarts.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o --- --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o --- [ 46%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/UFF/Params.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o --- [ 46%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/MMFF/AngleBend.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o --- [ 46%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/MMFF/BondStretch.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o --- [ 46%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/MMFF/StretchBend.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o --- [ 46%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp --- External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/all --- --- rdkit/Chem/rdCoordGen.so --- [ 46%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so cd /construction/science/rdkit/.build/External/CoordGen/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/rdkit/.build/lib /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so -pthread [ 46%] Built target rdCoordGen --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o --- --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o --- [ 46%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/MMFF/TorsionAngle.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o --- [ 47%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/MMFF/OopBend.cpp --- Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/all --- --- rdkit/Chem/rdCIPLabeler.so --- [ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitCIPLabeler.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 48%] Built target rdCIPLabeler --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o --- --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o --- --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o --- [ 48%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/MMFF/Nonbonded.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o --- [ 48%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/MMFF/DistanceConstraint.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o --- [ 48%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/MMFF/AngleConstraint.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o --- [ 48%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/MMFF/TorsionConstraint.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o --- --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o --- [ 48%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/MMFF/Params.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o --- [ 49%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/MMFF/PositionConstraint.cpp --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/all --- --- lib/libRDKitDepictor.so.1.2020.09.3 --- [ 49%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /construction/science/rdkit/.build/Code/GraphMol/Depictor && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2020.09.3 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolAlign.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/Depictor && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so [ 49%] Built target Depictor --- Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/all --- /usr/bin/make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend --- Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Depictor/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Depictor/Wrap /construction/science/rdkit/.build/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake Scanning dependencies of target rdDepictor /usr/bin/make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build --- Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o --- [ 49%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdDepictor_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- lib/libRDKitSmilesParse.so.1.2020.09.3 --- [ 49%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so [ 49%] Built target SmilesParse --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/all --- --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- --- Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/all --- --- Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/all --- /usr/bin/make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- /usr/bin/make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend --- Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/all --- /usr/bin/make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend --- Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/all --- /usr/bin/make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- /usr/bin/make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- /usr/bin/make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- /usr/bin/make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend --- Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/all --- --- Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend --- --- Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/all --- --- Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend --- --- Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ReducedGraphs /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Fingerprints /construction/science/rdkit/.build/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend --- --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/all --- --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend --- --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolChemicalFeatures /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemTransforms /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend --- --- Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Abbreviations /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Abbreviations /construction/science/rdkit/.build/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FragCatalog /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FragCatalog /construction/science/rdkit/.build/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FileParsers /construction/science/rdkit/.build/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FilterCatalog /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --- Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/all --- Scanning dependencies of target ReducedGraphs /usr/bin/make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build --- Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o --- [ 49%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DReducedGraphs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp --- Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/all --- Scanning dependencies of target Abbreviations /usr/bin/make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build --- Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o --- [ 49%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Abbreviations/Abbreviations.cpp --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- Scanning dependencies of target FilterCatalog /usr/bin/make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o --- [ 49%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- Scanning dependencies of target FragCatalog --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FilterCatalog/Filters.cpp --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- /usr/bin/make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/all --- Scanning dependencies of target ChemTransforms /usr/bin/make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o --- [ 49%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/all --- --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o --- [ 49%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- Scanning dependencies of target MolChemicalFeatures /usr/bin/make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o --- [ 49%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- Scanning dependencies of target Fingerprints /usr/bin/make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o --- [ 49%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/Mol2FileParser.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- lib/libRDKitForceField.so.1.2020.09.3 --- [ 49%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /construction/science/rdkit/.build/Code/ForceField && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2020.09.3 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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitOptimizer.so.1.2020.09.3 ../../lib/libRDKitTrajectory.so.1.2020.09.3 ../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/ForceField && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2020.09.3 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so [ 49%] Built target ForceField --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/all --- /usr/bin/make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ForceFieldHelpers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake Scanning dependencies of target ForceFieldHelpers /usr/bin/make -f 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-I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o --- [ 49%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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/construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o --- [ 49%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp --- Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/all --- --- rdkit/Chem/rdDepictor.so --- [ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /construction/science/rdkit/.build/Code/GraphMol/Depictor/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 50%] Built target rdDepictor --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o --- [ 50%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp --- Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/all --- --- lib/libRDKitReducedGraphs.so.1.2020.09.3 --- [ 50%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2020.09.3 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2020.09.3 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so [ 50%] Built target ReducedGraphs --- Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/all --- /usr/bin/make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend --- Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ReducedGraphs/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs/Wrap /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --- Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/all --- --- Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o --- [ 50%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp --- Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/all --- Scanning dependencies of target rdReducedGraphs /usr/bin/make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make 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-I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/all --- --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o --- [ 50%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/all --- --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o --- [ 51%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp --- Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/all --- --- lib/libRDKitAbbreviations.so.1.2020.09.3 --- [ 51%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so cd /construction/science/rdkit/.build/Code/GraphMol/Abbreviations && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2020.09.3 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/Abbreviations && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2020.09.3 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so [ 51%] Built target Abbreviations --- Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/all --- /usr/bin/make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend --- Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Abbreviations/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Abbreviations/Wrap /construction/science/rdkit/.build/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake Scanning dependencies of target rdAbbreviations /usr/bin/make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build --- Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o --- [ 51%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Abbreviations/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdAbbreviations_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o --- [ 51%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o --- [ 51%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o --- [ 51%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/all --- --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o --- [ 52%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o --- [ 52%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o --- [ 53%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FilterCatalog/FilterMatchers.cpp --- Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/all --- --- rdkit/Chem/rdReducedGraphs.so --- [ 53%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so cd /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitReducedGraphs.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 53%] Built target rdReducedGraphs --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o --- [ 54%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/AtomPairs.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o --- [ 54%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/MACCS.cpp --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/all --- --- lib/libRDKitChemTransforms.so.1.2020.09.3 --- [ 54%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so [ 55%] Built target ChemTransforms --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- /usr/bin/make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Wrap /construction/science/rdkit/.build/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o --- [ 55%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FragCatalog/FragCatParams.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- Scanning dependencies of target rdchem /usr/bin/make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o --- --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- --- lib/libRDKitMolChemicalFeatures.so.1.2020.09.3 --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- [ 55%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/rdchem.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/rdchem.cpp --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- [ 56%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.3 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so [ 56%] Built target MolChemicalFeatures --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/all --- /usr/bin/make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolChemicalFeatures/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures/Wrap /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake Scanning dependencies of target rdMolChemicalFeatures /usr/bin/make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o --- [ 56%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolChemicalFeatures_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o --- [ 56%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/MHFP.cpp --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o --- [ 56%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp --- Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/all --- --- rdkit/Chem/rdAbbreviations.so --- [ 56%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so cd /construction/science/rdkit/.build/Code/GraphMol/Abbreviations/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitAbbreviations.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/all --- --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o --- [ 56%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp --- Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/all --- [ 56%] Built target rdAbbreviations --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o --- [ 56%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/Table.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/Table.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o --- [ 56%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/all --- --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o --- [ 56%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o --- [ 56%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o --- [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/all --- --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o --- [ 56%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolChemicalFeatures_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/all --- --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o --- [ 56%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- --- lib/libRDKitFilterCatalog.so.1.2020.09.3 --- [ 56%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitCatalogs.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so [ 56%] Built target FilterCatalog --- Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/all --- /usr/bin/make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend --- Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FilterCatalog/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog/Wrap /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake Scanning dependencies of target rdfiltercatalog /usr/bin/make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build --- Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o --- [ 57%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdfiltercatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o --- [ 57%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o --- [ 57%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp --- Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/all --- --- Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o --- [ 57%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdfiltercatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o --- [ 58%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o --- [ 58%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/Atom.cpp --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- --- lib/libRDKitFragCatalog.so.1.2020.09.3 --- [ 58%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2020.09.3 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2020.09.3 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so [ 58%] Built target FragCatalog --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o --- [ 58%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o --- [ 58%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o --- cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wa--- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o --- cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wa--- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o --- ll -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/FingerprintUtil.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o --- ll -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/all --- --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o --- [ 58%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolChemicalFeatures_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/all --- --- lib/libRDKitForceFieldHelpers.so.1.2020.09.3 --- [ 58%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.3 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitForceField.so.1.2020.09.3 ../../../lib/libRDKitOptimizer.so.1.2020.09.3 ../../../lib/libRDKitTrajectory.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so [ 58%] Built target ForceFieldHelpers --- Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/all --- /usr/bin/make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend --- Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/ForceField/Wrap /construction/science/rdkit/.build/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake Scanning dependencies of target rdForceField /usr/bin/make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build --- Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o --- [ 58%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /construction/science/rdkit/.build/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdForceField_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/ForceField/Wrap/ForceField.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o --- [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/MolSGroupWriting.cpp --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/all --- --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o --- [ 59%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolChemicalFeatures_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o --- [ 60%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/Bond.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o --- [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/MolFileStereochem.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o --- [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/MolFileWriter.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- lib/libRDKitFingerprints.so.1.2020.09.3 --- [ 60%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2020.09.3 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so [ 60%] Built target Fingerprints --- Code/DistGeom/CMakeFiles/DistGeometry.dir/all --- /usr/bin/make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend --- Code/DistGeom/CMakeFiles/DistGeometry.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DistGeom /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/DistGeom /construction/science/rdkit/.build/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake Scanning dependencies of target DistGeometry /usr/bin/make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build --- Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o --- [ 60%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o cd /construction/science/rdkit/.build/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DistGeom/DistGeomUtils.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function 'std::__cxx11::string RDKit::SGroupWriting::BuildV2000SAPLines(int, const RDKit::SubstanceGroup&)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: warning: '%3d' directive output may be truncated writing between 3 and 11 bytes into a region of size 4 [-Wformat-truncation=] snprintf(output, 5, " %3d", value); ^~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-2147483647, 2147483647] /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:11: note: 'snprintf' output between 5 and 13 bytes into a destination of size 5 snprintf(output, 5, " %3d", value); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o --- [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o --- [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/SDMolSupplier.cpp --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/all --- --- rdkit/Chem/rdMolChemicalFeatures.so --- [ 61%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 61%] Built target rdMolChemicalFeatures --- Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/all --- /usr/bin/make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend --- Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ForceFieldHelpers/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/Wrap /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake Scanning dependencies of target rdForceFieldHelpers /usr/bin/make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build --- Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o --- [ 61%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdForceFieldHelpers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o --- [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/SDWriter.cpp --- Code/DistGeom/CMakeFiles/DistGeometry.dir/all --- --- Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o --- [ 61%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o cd /construction/science/rdkit/.build/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DistGeom/TriangleSmooth.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o --- [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp --- Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/all --- --- rdkit/ForceField/rdForceField.so --- [ 62%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /construction/science/rdkit/.build/Code/ForceField/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitForceField.so.1.2020.09.3 ../../../lib/libRDKitOptimizer.so.1.2020.09.3 ../../../lib/libRDKitTrajectory.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 62%] Built target rdForceField --- Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/all --- /usr/bin/make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend --- Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolAlign /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolAlign /construction/science/rdkit/.build/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake Scanning dependencies of target O3AAlign /usr/bin/make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build --- Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o --- [ 62%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o --- [ 62%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/Mol.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o --- [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/SmilesWriter.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o --- [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/TDTMolSupplier.cpp --- Code/DistGeom/CMakeFiles/DistGeometry.dir/all --- --- Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o --- [ 62%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o cd /construction/science/rdkit/.build/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS 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/construction/science/rdkit/rdkit-Release_2020_09_3/Code/DistGeom/DistViolationContrib.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o --- [ 62%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/Conformer.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o --- [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/TDTWriter.cpp --- Code/DistGeom/CMakeFiles/DistGeometry.dir/all --- --- Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o --- [ 62%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o cd /construction/science/rdkit/.build/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DistGeom/ChiralViolationContrib.cpp --- Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/all --- --- rdkit/Chem/rdfiltercatalog.so --- [ 62%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../../lib/libRDKitCatalogs.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 62%] Built target rdfiltercatalog --- Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/all --- /usr/bin/make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend --- Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Fingerprints/Wrap /construction/science/rdkit/.build/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake Scanning dependencies of target rdFingerprintGenerator /usr/bin/make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build --- Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o --- [ 63%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdFingerprintGenerator_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o --- [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/TplFileParser.cpp --- Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/all --- --- rdkit/Chem/rdForceFieldHelpers.so --- [ 64%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitForceField.so.1.2020.09.3 ../../../../lib/libRDKitOptimizer.so.1.2020.09.3 ../../../../lib/libRDKitTrajectory.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 64%] Built target rdForceFieldHelpers --- Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/all --- /usr/bin/make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend --- Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Fingerprints/Wrap /construction/science/rdkit/.build/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake Scanning dependencies of target rdMHFPFingerprint /usr/bin/make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build --- Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o --- [ 65%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMHFPFingerprint_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp --- Code/DistGeom/CMakeFiles/DistGeometry.dir/all --- --- lib/libRDKitDistGeometry.so.1.2020.09.3 --- [ 65%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /construction/science/rdkit/.build/Code/DistGeom && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2020.09.3 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2020.09.3 ../../lib/libRDKitForceField.so.1.2020.09.3 ../../lib/libRDKitOptimizer.so.1.2020.09.3 ../../lib/libRDKitTrajectory.so.1.2020.09.3 ../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread cd /construction/science/rdkit/.build/Code/DistGeom && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2020.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so [ 66%] Built target DistGeometry --- Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/all --- /usr/bin/make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend --- Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SubstructLibrary /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake Scanning dependencies of target SubstructLibrary /usr/bin/make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build --- Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o --- [ 66%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSubstructLibrary_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o --- [ 66%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/TplFileWriter.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o --- [ 67%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/PDBParser.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o --- [ 67%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/PDBWriter.cpp --- Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/all --- --- lib/libRDKitO3AAlign.so.1.2020.09.3 --- [ 67%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2020.09.3 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitForceField.so.1.2020.09.3 ../../../lib/libRDKitOptimizer.so.1.2020.09.3 ../../../lib/libRDKitTrajectory.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2020.09.3 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so [ 67%] Built target O3AAlign --- Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/all --- /usr/bin/make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend --- Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DistGeom/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/DistGeom/Wrap /construction/science/rdkit/.build/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake Scanning dependencies of target DistGeom /usr/bin/make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build --- Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o --- [ 68%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /construction/science/rdkit/.build/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/DistGeom/Wrap/DistGeom.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o --- [ 68%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/PDBSupplier.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o --- [ 68%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/RingInfo.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o --- [ 68%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/XYZFileWriter.cpp --- Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/all --- --- rdkit/Chem/rdFingerprintGenerator.so --- [ 68%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 68%] Built target rdFingerprintGenerator --- Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/all --- /usr/bin/make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend --- Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/DistGeomHelpers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake Scanning dependencies of target DistGeomHelpers /usr/bin/make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build --- Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o --- [ 68%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o --- [ 68%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/MaeMolSupplier.cpp --- Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/all --- --- Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o --- [ 68%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DSubstructLibrary_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SubstructLibrary/PatternFactory.cpp --- 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-I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/ProximityBonds.cpp --- Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/all --- --- rdkit/DistanceGeometry/DistGeom.so --- [ 68%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /construction/science/rdkit/.build/Code/DistGeom/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitDistGeometry.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.3 ../../../lib/libRDKitForceField.so.1.2020.09.3 ../../../lib/libRDKitOptimizer.so.1.2020.09.3 ../../../lib/libRDKitTrajectory.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 68%] Built target DistGeom --- Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/all --- --- Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o --- [ 68%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/DistGeomHelpers/Embedder.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o --- [ 68%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/SequenceParsers.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o --- [ 68%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/EditableMol.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o --- [ 69%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/SequenceWriters.cpp --- Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/all --- --- rdkit/Chem/rdMHFPFingerprint.so --- [ 69%] Linking CXX shared module 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../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 69%] Built target rdMHFPFingerprint --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o --- [ 69%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/MonomerInfo.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o --- [ 69%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/SVGParser.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o --- [ 69%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/PNGParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/PNGParser.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o --- [ 69%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp --- Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/all --- --- lib/libRDKitSubstructLibrary.so.1.2020.09.3 --- [ 69%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2020.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitCatalogs.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2020.09.3 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so [ 69%] Built target SubstructLibrary --- Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/all --- /usr/bin/make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend --- Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SubstructLibrary/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary/Wrap /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake Scanning dependencies of target rdSubstructLibrary /usr/bin/make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build --- Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o --- [ 69%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdSubstructLibrary_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o --- [ 69%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp --- Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/all --- --- lib/libRDKitDistGeomHelpers.so.1.2020.09.3 --- [ 69%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.3 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDistGeometry.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitForceField.so.1.2020.09.3 ../../../lib/libRDKitOptimizer.so.1.2020.09.3 ../../../lib/libRDKitTrajectory.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so [ 70%] Built target DistGeomHelpers --- Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/all --- --- Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o --- [ 70%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdSubstructLibrary_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o --- [ 71%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o --- [ 71%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o --- [ 71%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/MolBundle.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o --- [ 71%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/StereoGroup.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/StereoGroup.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o --- [ 71%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/SubstanceGroup.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o --- [ 71%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/Chirality.cpp --- Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/all --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:34: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII) { ~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if ((!df_isTextMode || c <= STD_ASCII) && ~~^~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII && ~~^~~~~~~~~~~ --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all --- --- lib/libRDKitFileParsers.so.1.2020.09.3 --- [ 72%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2020.09.3 CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDWriter.cpp.o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o CMakeFiles/FileParsers.dir/PDBParser.cpp.o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o CMakeFiles/FileParsers.dir/SVGParser.cpp.o CMakeFiles/FileParsers.dir/PNGParser.cpp.o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so [ 72%] Built target FileParsers --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/all --- --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/all --- --- Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/all --- /usr/bin/make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/all --- /usr/bin/make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- /usr/bin/make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend --- Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/all --- --- Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/DistGeomHelpers/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers/Wrap /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/all --- --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend --- --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend --- --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FMCS /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FMCS /construction/science/rdkit/.build/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Descriptors /construction/science/rdkit/.build/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FragCatalog/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FragCatalog/Wrap /construction/science/rdkit/.build/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --- Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/all --- Scanning dependencies of target rdDistGeom /usr/bin/make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build --- Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o --- [ 73%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdDistGeom_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/all --- Scanning dependencies of target FMCS /usr/bin/make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- Scanning dependencies of target rdfragcatalog /usr/bin/make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/all --- --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o --- [ 73%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FMCS/FMCS.cpp --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o --- [ 73%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdfragcatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- Scanning dependencies of target Descriptors /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o --- [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Descriptors.dir/Crippen.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/Crippen.cpp --- Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/all --- --- rdkit/Chem/rdSubstructLibrary.so --- [ 73%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitSubstructLibrary.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 73%] Built target rdSubstructLibrary --- Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/all --- /usr/bin/make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend --- Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MMPA /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MMPA /construction/science/rdkit/.build/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake Scanning dependencies of target MMPA /usr/bin/make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build --- Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o --- [ 73%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MMPA/MMPA.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- /usr/bin/make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Wrap /construction/science/rdkit/.build/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o --- [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/MolDescriptors.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o --- [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/BCUT.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- Scanning dependencies of target rdmolfiles /usr/bin/make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o --- [ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/rdmolfiles.cpp --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o --- [ 73%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdfragcatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o --- [ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o --- [ 74%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/MolSurf.cpp --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/all --- --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o --- [ 74%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FMCS/Seed.cpp --- Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/all --- --- lib/libRDKitMMPA.so.1.2020.09.3 --- [ 74%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /construction/science/rdkit/.build/Code/GraphMol/MMPA && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2020.09.3 CMakeFiles/MMPA.dir/MMPA.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/MMPA && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2020.09.3 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so [ 75%] Built target MMPA --- Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/all --- /usr/bin/make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend --- Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MMPA/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MMPA/Wrap /construction/science/rdkit/.build/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake Scanning dependencies of target rdMMPA /usr/bin/make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o --- [ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/Lipinski.cpp --- Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/all --- --- Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o --- [ 75%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMMPA_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Conformer.h:14, from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/RDKitBase.h:25, from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/SubstanceGroup.cpp:17: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h: In function 'void RDKit::{anonymous}::addBracketHelper(RDKit::SubstanceGroup&, boost::python::api::object)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:31: warning: '*((void*)(&)+32).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:43: warning: '*((void*)(&)+32).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:58:55: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:22: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII) { ~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if ((!df_isTextMode || c <= STD_ASCII) && ~~^~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII && ~~^~~~~~~~~~~ --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o --- [ 76%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdfragcatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o --- [ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/all --- --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o --- [ 78%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- rdkit/Chem/rdchem.so --- [ 78%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 78%] Built target rdchem --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o --- [ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/MQN.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o --- [ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/Property.cpp --- Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/all --- --- rdkit/Chem/rdDistGeom.so --- [ 78%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdDistGeom.so 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../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 78%] Built target rdDistGeom --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o --- [ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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-I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o --- [ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 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-O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/AtomFeat.cpp --- Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/all --- --- rdkit/Chem/rdMMPA.so --- [ 79%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /construction/science/rdkit/.build/Code/GraphMol/MMPA/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o 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/construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII && ~~^~~~~~~~~~~ --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o --- [ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 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-fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/GETAWAY.cpp --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o --- [ 80%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdfragcatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External 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-fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/WHIM.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o --- [ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/CoulombMat.cpp --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/all --- --- lib/libRDKitFMCS.so.1.2020.09.3 --- [ 80%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2020.09.3 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2020.09.3 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so [ 80%] Built target FMCS --- Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/all --- /usr/bin/make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend --- Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FMCS/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FMCS/Wrap /construction/science/rdkit/.build/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake Scanning dependencies of target rdFMCS /usr/bin/make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build --- Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o --- [ 80%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdFMCS_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o --- [ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o --- cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/TDTMolSupplier.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o --- [ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/SmilesMolSupplier.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o --- [ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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/construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/SmilesWriter.cpp --- Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/all --- /usr/bin/make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend --- Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/RGroupDecomposition /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake Scanning dependencies of target RGroupDecomposition /usr/bin/make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build --- Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o --- [ 80%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DRGroupDecomposition_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- --- rdkit/Chem/rdfragcatalog.so --- [ 80%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitFragCatalog.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 80%] Built target rdfragcatalog --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o --- [ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/SDWriter.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o --- [ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/TDTWriter.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/SmilesWriter.cpp:20: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII) { ~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if ((!df_isTextMode || c <= STD_ASCII) && ~~^~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII && ~~^~~~~~~~~~~ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o --- [ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/PDBWriter.cpp --- Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/all --- --- Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o --- [ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DRGroupDecomposition_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o --- [ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o --- [ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/SDWriter.cpp:21: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII) { ~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if ((!df_isTextMode || c <= STD_ASCII) && ~~^~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII && ~~^~~~~~~~~~~ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/TDTWriter.cpp:21: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII) { ~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if ((!df_isTextMode || c <= STD_ASCII) && ~~^~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII && ~~^~~~~~~~~~~ --- Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/all --- --- Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o --- [ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DRGroupDecomposition_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/PDBWriter.cpp:20: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII) { ~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if ((!df_isTextMode || c <= STD_ASCII) && ~~^~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII && ~~^~~~~~~~~~~ --- Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/all --- --- Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o --- [ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DRGroupDecomposition_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- lib/libRDKitDescriptors.so.1.2020.09.3 --- [ 81%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2020.09.3 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o CMakeFiles/Descriptors.dir/EEM.cpp.o CMakeFiles/Descriptors.dir/PBF.cpp.o CMakeFiles/Descriptors.dir/PMI.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o CMakeFiles/Descriptors.dir/RDF.cpp.o CMakeFiles/Descriptors.dir/MORSE.cpp.o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o CMakeFiles/Descriptors.dir/WHIM.cpp.o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so [ 81%] Built target Descriptors --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- --- Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- /usr/bin/make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- /usr/bin/make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend --- Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/all --- /usr/bin/make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend --- --- Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/all --- --- Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend --- --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Descriptors/Wrap /construction/science/rdkit/.build/Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/DependInfo.cmake --- Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolAlign/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolAlign/Wrap /construction/science/rdkit/.build/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ChemReactions /construction/science/rdkit/.build/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake --- Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/all --- Scanning dependencies of target rdMolAlign /usr/bin/make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build --- Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o --- [ 81%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolAlign_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- Scanning dependencies of target rdMolDescriptors /usr/bin/make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o --- [ 81%] Building CXX object Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolDescriptors_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/MultithreadedMolSupplier.h:15, from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp:23: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII) { ~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if ((!df_isTextMode || c <= STD_ASCII) && ~~^~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII && ~~^~~~~~~~~~~ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/MultithreadedMolSupplier.h:15, from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp:23: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII) { ~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if ((!df_isTextMode || c <= STD_ASCII) && ~~^~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII && ~~^~~~~~~~~~~ --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- Scanning dependencies of target ChemReactions /usr/bin/make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o --- [ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/Reaction.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o --- [ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/MDLParser.cpp --- Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/all --- /usr/bin/make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend --- Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolHash /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolHash /construction/science/rdkit/.build/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake Scanning dependencies of target MolHash /usr/bin/make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build --- Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o --- --- Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o --- --- Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o --- [ 81%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolHash/hashfunctions.cpp --- Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o --- [ 81%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolHash/normalize.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- --- rdkit/Chem/rdmolfiles.so --- [ 81%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so -pthread [ 81%] Built target rdmolfiles --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o --- [ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/DaylightParser.cpp --- Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/all --- --- lib/libRDKitRGroupDecomposition.so.1.2020.09.3 --- [ 82%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2020.09.3 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitFMCS.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2020.09.3 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so [ 83%] Built target RGroupDecomposition --- Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/all --- /usr/bin/make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend --- Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/RGroupDecomposition/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition/Wrap /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake Scanning dependencies of target rdRGroupDecomposition /usr/bin/make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build --- Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o --- [ 84%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdRGroupDecomposition_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o --- [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/ReactionPickler.cpp --- Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/all --- --- rdkit/Chem/rdFMCS.so --- [ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so cd /construction/science/rdkit/.build/Code/GraphMol/FMCS/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitFMCS.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 84%] Built target rdFMCS --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o --- [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/ReactionWriter.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o --- [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/ReactionDepict.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o --- [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o --- [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/ReactionUtils.cpp --- Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/all --- --- lib/libRDKitMolHash.so.1.2020.09.3 --- [ 84%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /construction/science/rdkit/.build/Code/GraphMol/MolHash && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2020.09.3 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/MolHash && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2020.09.3 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so [ 84%] Built target MolHash --- Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/all --- /usr/bin/make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend --- Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolHash/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolHash/Wrap /construction/science/rdkit/.build/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o --- [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/MoleculeParser.cpp --- Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/all --- Scanning dependencies of target rdMolHash /usr/bin/make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build --- Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o --- [ 84%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolHash_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o --- [ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/ReactionRunner.cpp --- Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/all --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp:47: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII) { ~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if ((!df_isTextMode || c <= STD_ASCII) && ~~^~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII && ~~^~~~~~~~~~~ --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o --- [ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/PreprocessRxn.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o --- [ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/SanitizeRxn.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o --- [ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/PNGParser.cpp --- Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/all --- --- rdkit/Chem/rdMolAlign.so --- [ 85%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitO3AAlign.so.1.2020.09.3 ../../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.3 ../../../../lib/libRDKitForceField.so.1.2020.09.3 ../../../../lib/libRDKitOptimizer.so.1.2020.09.3 ../../../../lib/libRDKitTrajectory.so.1.2020.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 85%] Built target rdMolAlign --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o --- [ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o --- [ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o --- cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o --- cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Conformer.h:14, from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ROMol.h:36, from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/GraphMol.h:19, from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:12: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h: In function 'boost::python::list {anonymous}::GetUSRDistributionsFromPoints(boost::python::api::object, boost::python::api::object)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:87:15: warning: '*((void*)(&)+32).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] x = other.x; ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:88:15: warning: '*((void*)(&)+32).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] y = other.y; ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:89:15: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] z = other.z; ~~~~~~^ --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o --- [ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h: In function 'boost::python::list {anonymous}::GetUSRDistributions(boost::python::api::object, boost::python::api::object)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:87:15: warning: '*((void*)(&)+32).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] x = other.x; ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:88:15: warning: '*((void*)(&)+32).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] y = other.y; ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:89:15: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] z = other.z; ~~~~~~^ --- Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/all --- --- rdkit/Chem/rdRGroupDecomposition.so --- [ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitRGroupDecomposition.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitFMCS.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 86%] Built target rdRGroupDecomposition --- Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/all --- --- rdkit/Chem/rdMolHash.so --- [ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /construction/science/rdkit/.build/Code/GraphMol/MolHash/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitMolHash.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 87%] Built target rdMolHash --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- --- rdkit/Chem/rdMolDescriptors.so --- [ 87%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 87%] Built target rdMolDescriptors --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- lib/libRDKitChemReactions.so.1.2020.09.3 --- [ 87%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2020.09.3 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/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so [ 87%] Built target ChemReactions --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/all --- --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- --- Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/all --- --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/all --- /usr/bin/make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- /usr/bin/make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend --- Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/all --- /usr/bin/make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend --- Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/all --- /usr/bin/make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ChemReactions/Wrap /construction/science/rdkit/.build/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend --- --- Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/all --- --- Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolStandardize /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolDraw2D /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --- Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/all --- --- Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Deprotect /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Deprotect /construction/science/rdkit/.build/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake --- Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolEnumerator /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolEnumerator /construction/science/rdkit/.build/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --- Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/all --- Scanning dependencies of target Deprotect /usr/bin/make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build --- Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o --- [ 87%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Deprotect/Deprotect.cpp --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/all --- Scanning dependencies of target rdChemReactions /usr/bin/make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o --- --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o --- --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o --- [ 87%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdChemReactions_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o --- [ 87%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdChemReactions_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 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Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o --- Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o --- [ 87%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp --- Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o --- cd /construction/science/rdkit/.build/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION 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-I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/MolStandardize.cpp --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o --- [ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o cd 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-I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/Metal.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o --- [ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/Normalize.cpp --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o --- [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -isystem /usr/local/include/freetype2 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp --- Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/all --- --- lib/libRDKitDeprotect.so.1.2020.09.3 --- [ 89%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so cd /construction/science/rdkit/.build/Code/GraphMol/Deprotect && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitDeprotect.so.1 -o ../../../lib/libRDKitDeprotect.so.1.2020.09.3 CMakeFiles/Deprotect.dir/Deprotect.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread /usr/local/lib/libboost_serialization.so cd /construction/science/rdkit/.build/Code/GraphMol/Deprotect && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2020.09.3 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so [ 89%] Built target Deprotect --- Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/all --- /usr/bin/make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend --- Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Deprotect/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Deprotect/Wrap /construction/science/rdkit/.build/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake --- Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/all --- --- lib/libRDKitMolEnumerator.so.1.2020.09.3 --- [ 89%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so cd /construction/science/rdkit/.build/Code/GraphMol/MolEnumerator && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2020.09.3 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/local/lib/libboost_serialization.so cd /construction/science/rdkit/.build/Code/GraphMol/MolEnumerator && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2020.09.3 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so [ 90%] Built target MolEnumerator --- Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/all --- /usr/bin/make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend --- Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolEnumerator/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolEnumerator/Wrap /construction/science/rdkit/.build/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --- Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/all --- Scanning dependencies of target rdDeprotect /usr/bin/make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build --- Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o --- [ 90%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdDeprotect_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp --- Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/all --- Scanning dependencies of target rdMolEnumerator /usr/bin/make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build --- Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o --- [ 90%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolEnumerator_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o --- [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/Validate.cpp --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o --- [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -isystem /usr/local/include/freetype2 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o --- [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -isystem /usr/local/include/freetype2 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolDraw2D/DrawTextJS.cpp --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o --- [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -isystem /usr/local/include/freetype2 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolDraw2D/DrawTextFT.cpp --- Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/all --- --- Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o --- [ 90%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdDeprotect_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o --- [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -isystem /usr/local/include/freetype2 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o --- [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD 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/construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/Charge.cpp --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o --- [ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -isystem /usr/local/include/freetype2 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o --- [ 91%] Building CXX object 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-I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/Tautomer.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o --- cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/Fragment.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o --- [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- --- lib/libRDKitMolDraw2D.so.1.2020.09.3 --- [ 92%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2020.09.3 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitChemReactions.so.1.2020.09.3 /usr/local/lib/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/local/lib/libboost_serialization.so cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2020.09.3 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so [ 92%] Built target MolDraw2D --- Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/all --- /usr/bin/make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend --- Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolDraw2D/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D/Wrap /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake Scanning dependencies of target rdMolDraw2D /usr/bin/make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build --- Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o --- [ 92%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolDraw2D_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -isystem /usr/local/include/freetype2 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp --- Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/all --- --- rdkit/Chem/rdMolEnumerator.so --- [ 92%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so cd /construction/science/rdkit/.build/Code/GraphMol/MolEnumerator/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitMolEnumerator.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 92%] Built target rdMolEnumerator --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/all --- /usr/bin/make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Wrap /construction/science/rdkit/.build/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o --- [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/all --- Scanning dependencies of target rdmolops /usr/bin/make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o --- [ 93%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o --- [ 93%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdmolops_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -isystem /usr/local/include/freetype2 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unuse--- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o --- cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdmolops_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -isystem /usr/local/include/freetype2 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/MolOps.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o --- d-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/rdmolops.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o --- [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp --- Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/all --- --- rdkit/Chem/rdDeprotect.so --- [ 93%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so cd /construction/science/rdkit/.build/Code/GraphMol/Deprotect/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitDeprotect.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 93%] Built target rdDeprotect --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o --- [ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Drdmolops_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -isystem /usr/local/include/freetype2 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/ChiralityOps.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Wrap/MolOps.cpp:30: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII) { ~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if ((!df_isTextMode || c <= STD_ASCII) && ~~^~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (df_isTextMode && c > STD_ASCII && ~~^~~~~~~~~~~ --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o --- [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o --- [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o --- [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/all --- --- rdkit/Chem/rdChemReactions.so --- [ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 95%] Built target rdChemReactions --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- lib/libRDKitMolStandardize.so.1.2020.09.3 --- [ 95%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2020.09.3 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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_serialization.so cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2020.09.3 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so [ 95%] Built target MolStandardize --- Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/all --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/all --- --- Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/all --- --- Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/all --- /usr/bin/make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/all --- /usr/bin/make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend --- Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/all --- /usr/bin/make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend --- Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/all --- --- Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/TautomerQuery /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/TautomerQuery /construction/science/rdkit/.build/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend --- --- Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/all --- --- Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/Wrap /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake --- Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ScaffoldNetwork /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ScaffoldNetwork /construction/science/rdkit/.build/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake --- Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/all --- Scanning dependencies of target TautomerQuery /usr/bin/make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build --- Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o --- [ 95%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DTautomerQuery_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/TautomerQuery/TautomerQuery.cpp --- Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/all --- Scanning dependencies of target ScaffoldNetwork /usr/bin/make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build --- Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o --- [ 96%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DScaffoldNetwork_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/all --- Scanning dependencies of target rdMolStandardize /usr/bin/make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o --- [ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o --- [ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o --- cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolStandardize_EXPORTS 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/usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolStandardize_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC 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-I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o --- [ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolStandardize_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o --- [ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolStandardize_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o --- [ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolStandardize_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/all --- --- rdkit/Chem/rdmolops.so --- [ 97%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolDraw2D.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitPartialCharges.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 /usr/local/lib/libfreetype.so /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 97%] Built target rdmolops --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o --- [ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdMolStandardize_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp --- Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/all --- In file included from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/Conformer.h:14, from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ROMol.h:36, from /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:17: /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = RDGeom::Point2D]': /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:269:57: warning: '*((void*)(&)+32).RDGeom::Point2D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] Point2D(const Point2D &other) : Point(other), x(other.x), y(other.y) {} ~~~~~~^ /construction/science/rdkit/rdkit-Release_2020_09_3/Code/Geometry/point.h:269:69: warning: '*((void*)(&)+32).RDGeom::Point2D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] Point2D(const Point2D &other) : Point(other), x(other.x), y(other.y) {} ~~~~~~^ --- rdkit/Chem/Draw/rdMolDraw2D.so --- [ 98%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitMolDraw2D.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 /usr/local/lib/libfreetype.so /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 98%] Built target rdMolDraw2D --- Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/all --- --- lib/libRDKitScaffoldNetwork.so.1.2020.09.3 --- [ 98%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so cd /construction/science/rdkit/.build/Code/GraphMol/ScaffoldNetwork && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.3 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolStandardize.so.1.2020.09.3 ../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../lib/libRDKitFingerprints.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/ScaffoldNetwork && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.3 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so [ 98%] Built target ScaffoldNetwork --- Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/all --- /usr/bin/make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend --- Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ScaffoldNetwork/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ScaffoldNetwork/Wrap /construction/science/rdkit/.build/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake Scanning dependencies of target rdScaffoldNetwork /usr/bin/make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build --- Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o --- [ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdScaffoldNetwork_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp --- Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/all --- --- lib/libRDKitTautomerQuery.so.1.2020.09.3 --- [ 98%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so cd /construction/science/rdkit/.build/Code/GraphMol/TautomerQuery && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2020.09.3 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolStandardize.so.1.2020.09.3 ../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../lib/libRDKitFingerprints.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/TautomerQuery && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2020.09.3 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so [ 98%] Built target TautomerQuery --- Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/all --- /usr/bin/make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend --- Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2020_09_3 /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/TautomerQuery/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/TautomerQuery/Wrap /construction/science/rdkit/.build/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake Scanning dependencies of target rdTautomerQuery /usr/bin/make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build --- Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o --- [ 99%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdTautomerQuery_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2020_09_3/External -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2020_09_3/Code -I/construction/science/rdkit/rdkit-Release_2020_09_3/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -std=gnu++11 -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /construction/science/rdkit/rdkit-Release_2020_09_3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp --- rdkit/Chem/rdTautomerQuery.so --- [ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so cd /construction/science/rdkit/.build/Code/GraphMol/TautomerQuery/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitTautomerQuery.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2020.09.3 ../../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../../lib/libRDKitFingerprints.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [ 99%] Built target rdTautomerQuery --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/all --- --- rdkit/Chem/MolStandardize/rdMolStandardize.so --- [ 99%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitMolStandardize.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../../lib/libRDKitFingerprints.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [100%] Built target rdMolStandardize --- Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/all --- --- rdkit/Chem/Scaffolds/rdScaffoldNetwork.so --- [100%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so cd /construction/science/rdkit/.build/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2020.09.3 ../../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl [100%] Built target rdScaffoldNetwork /usr/local/bin/cmake -E cmake_progress_start /construction/science/rdkit/.build/CMakeFiles 0 SUCCEEDED 00:24:43 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> rdkit-2020.09.3 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> rdkit-2020.09.3 depends on package: py37-pillow>=7.0.0 - found ===> rdkit-2020.09.3 depends on package: py37-matplotlib>0 - found ===> rdkit-2020.09.3 depends on package: py37-reportlab>0 - found ===> rdkit-2020.09.3 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for rdkit-2020.09.3 ===> rdkit-2020.09.3 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> rdkit-2020.09.3 depends on package: py37-pillow>=7.0.0 - found ===> rdkit-2020.09.3 depends on package: py37-matplotlib>0 - found ===> rdkit-2020.09.3 depends on package: py37-reportlab>0 - found ===> rdkit-2020.09.3 depends on file: /usr/local/bin/python3.7 - found ===> Generating temporary packing list /usr/local/bin/cmake -S/construction/science/rdkit/rdkit-Release_2020_09_3 -B/construction/science/rdkit/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/science/rdkit/.build/CMakeFiles 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CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLutility.c.o CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RingDecomposerLib.c.o -pthread cd /construction/science/rdkit/.build/External/RingFamilies && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitRingDecomposerLib.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitRingDecomposerLib.so.1 CMakeFiles/CMakeRelink.dir/libRDKitRingDecomposerLib.so /usr/bin/make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitRDGeneral.so cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitRDGeneral.so.1.2020.09.3 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl -pthread cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitRDGeneral.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitRDGeneral.so.1 CMakeFiles/CMakeRelink.dir/libRDKitRDGeneral.so /usr/bin/make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitRDBoost.so cd /construction/science/rdkit/.build/Code/RDBoost && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitRDBoost.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitRDBoost.so.1.2020.09.3 CMakeFiles/RDBoost.dir/Wrap.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so cd /construction/science/rdkit/.build/Code/RDBoost && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitRDBoost.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitRDBoost.so.1 CMakeFiles/CMakeRelink.dir/libRDKitRDBoost.so /usr/bin/make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdBase.so cd /construction/science/rdkit/.build/Code/RDBoost/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/relink.txt --verbose=1 /usr/bin/c++ 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CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDBoost.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/bin/make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitRDGeometryLib.so cd /construction/science/rdkit/.build/Code/Geometry && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitRDGeometryLib.so.1.2020.09.3 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/Geometry && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitRDGeometryLib.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitRDGeometryLib.so.1 CMakeFiles/CMakeRelink.dir/libRDKitRDGeometryLib.so /usr/bin/make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdGeometry.so cd /construction/science/rdkit/.build/Code/Geometry/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing 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Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitEigenSolvers.so cd /construction/science/rdkit/.build/Code/Numerics/EigenSolvers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitEigenSolvers.so.1.2020.09.3 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/Numerics/EigenSolvers && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitEigenSolvers.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitEigenSolvers.so.1 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CMakeFiles/CMakeRelink.dir/libRDKitForceField.so.1.2020.09.3 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 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../../../lib/libRDKitOptimizer.so.1.2020.09.3 ../../../lib/libRDKitTrajectory.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/bin/make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitCatalogs.so cd /construction/science/rdkit/.build/Code/Catalogs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 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CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitFingerprints.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitFingerprints.so.1 CMakeFiles/CMakeRelink.dir/libRDKitFingerprints.so /usr/bin/make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/preinstall Linking CXX shared module 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CMakeFiles/CMakeRelink.dir/libRDKitPartialCharges.so.1 CMakeFiles/CMakeRelink.dir/libRDKitPartialCharges.so /usr/bin/make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdPartialCharges.so cd /construction/science/rdkit/.build/Code/GraphMol/PartialCharges/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o CMakeFiles/CMakeRelink.dir/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitPartialCharges.so.1.2020.09.3 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CMakeFiles/CMakeRelink.dir/libRDKitMolTransforms.so.1.2020.09.3 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/MolTransforms && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitMolTransforms.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitMolTransforms.so.1 CMakeFiles/CMakeRelink.dir/libRDKitMolTransforms.so /usr/bin/make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdMolTransforms.so cd 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../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitDistGeomHelpers.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitDistGeomHelpers.so.1 CMakeFiles/CMakeRelink.dir/libRDKitDistGeomHelpers.so /usr/bin/make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdDistGeom.so cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib 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../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/bin/make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitO3AAlign.so cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated 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/construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitO3AAlign.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitO3AAlign.so.1 CMakeFiles/CMakeRelink.dir/libRDKitO3AAlign.so /usr/bin/make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitMolAlign.so cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolAlign.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitMolAlign.so.1.2020.09.3 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitMolAlign.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitMolAlign.so.1 CMakeFiles/CMakeRelink.dir/libRDKitMolAlign.so /usr/bin/make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdMolAlign.so cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign/Wrap && /usr/local/bin/cmake -E cmake_link_script 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Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitMolChemicalFeatures.so cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitMolChemicalFeatures.so.1.2020.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o 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CMakeFiles/CMakeRelink.dir/libRDKitShapeHelpers.so.1.2020.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitShapeHelpers.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitShapeHelpers.so.1 CMakeFiles/CMakeRelink.dir/libRDKitShapeHelpers.so /usr/bin/make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdShapeHelpers.so cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o CMakeFiles/CMakeRelink.dir/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitShapeHelpers.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 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../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/local/lib/libboost_serialization.so cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitMolDraw2D.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitMolDraw2D.so.1 CMakeFiles/CMakeRelink.dir/libRDKitMolDraw2D.so /usr/bin/make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdMolDraw2D.so cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D/Wrap && /usr/local/bin/cmake -E cmake_link_script 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../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitFMCS.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitFMCS.so.1 CMakeFiles/CMakeRelink.dir/libRDKitFMCS.so /usr/bin/make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdFMCS.so cd /construction/science/rdkit/.build/Code/GraphMol/FMCS/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o CMakeFiles/CMakeRelink.dir/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitFMCS.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 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cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitMolHash.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitMolHash.so.1 CMakeFiles/CMakeRelink.dir/libRDKitMolHash.so /usr/bin/make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdMolHash.so cd /construction/science/rdkit/.build/Code/GraphMol/MolHash/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o CMakeFiles/CMakeRelink.dir/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitMolHash.so.1.2020.09.3 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CMakeFiles/CMakeRelink.dir/libRDKitMMPA.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitMMPA.so.1 CMakeFiles/CMakeRelink.dir/libRDKitMMPA.so /usr/bin/make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdMMPA.so cd /construction/science/rdkit/.build/Code/GraphMol/MMPA/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o CMakeFiles/CMakeRelink.dir/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitMMPA.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 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/construction/science/rdkit/.build/Code/GraphMol/CIPLabeler && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitCIPLabeler.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitCIPLabeler.so.1 CMakeFiles/CMakeRelink.dir/libRDKitCIPLabeler.so /usr/bin/make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdCIPLabeler.so cd /construction/science/rdkit/.build/Code/GraphMol/CIPLabeler/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o CMakeFiles/CMakeRelink.dir/rdCIPLabeler.so 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-fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitDeprotect.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitDeprotect.so.1.2020.09.3 CMakeFiles/Deprotect.dir/Deprotect.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 ../../../lib/libRDKitDescriptors.so.1.2020.09.3 ../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../lib/libRDKitPartialCharges.so.1.2020.09.3 ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread /usr/local/lib/libboost_serialization.so cd /construction/science/rdkit/.build/Code/GraphMol/Deprotect && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitDeprotect.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitDeprotect.so.1 CMakeFiles/CMakeRelink.dir/libRDKitDeprotect.so /usr/bin/make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdDeprotect.so cd /construction/science/rdkit/.build/Code/GraphMol/Deprotect/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o CMakeFiles/CMakeRelink.dir/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitDeprotect.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so 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../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/bin/make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitReducedGraphs.so cd /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitReducedGraphs.so.1.2020.09.3 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitReducedGraphs.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitReducedGraphs.so.1 CMakeFiles/CMakeRelink.dir/libRDKitReducedGraphs.so /usr/bin/make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdReducedGraphs.so cd /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o CMakeFiles/CMakeRelink.dir/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitReducedGraphs.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/bin/make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitTrajectory.so cd /construction/science/rdkit/.build/Code/GraphMol/Trajectory && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitTrajectory.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitTrajectory.so.1.2020.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -ldl ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Trajectory && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitTrajectory.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitTrajectory.so.1 CMakeFiles/CMakeRelink.dir/libRDKitTrajectory.so /usr/bin/make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitSubstructLibrary.so cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitSubstructLibrary.so.1.2020.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitCatalogs.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitSubstructLibrary.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitSubstructLibrary.so.1 CMakeFiles/CMakeRelink.dir/libRDKitSubstructLibrary.so /usr/bin/make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdSubstructLibrary.so cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o CMakeFiles/CMakeRelink.dir/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitSubstructLibrary.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitFingerprints.so.1.2020.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../../lib/libRDKitCatalogs.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 /usr/local/lib/libboost_serialization.so /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/bin/make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitRGroupDecomposition.so cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitRGroupDecomposition.so.1.2020.09.3 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../lib/libRDKitFMCS.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitAlignment.so.1.2020.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitRGroupDecomposition.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitRGroupDecomposition.so.1 CMakeFiles/CMakeRelink.dir/libRDKitRGroupDecomposition.so /usr/bin/make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdRGroupDecomposition.so cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -shared -o CMakeFiles/CMakeRelink.dir/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitRGroupDecomposition.so.1.2020.09.3 ../../../../lib/libRDKitRDBoost.so.1.2020.09.3 ../../../../lib/libRDKitFMCS.so.1.2020.09.3 ../../../../lib/libRDKitFileParsers.so.1.2020.09.3 ../../../../lib/libRDKitDepictor.so.1.2020.09.3 ../../../../lib/libRDKitMolAlign.so.1.2020.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../../lib/libRDKitAlignment.so.1.2020.09.3 /usr/local/lib/libcoordgen.so /usr/local/lib/libmaeparser.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.3 ../../../../lib/libRDKitGraphMol.so.1.2020.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 /usr/local/lib/libpython3.7m.so /usr/local/lib/libboost_python37.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/bin/make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitMolInterchange.so cd /construction/science/rdkit/.build/Code/GraphMol/MolInterchange && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o 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Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitScaffoldNetwork.so cd /construction/science/rdkit/.build/Code/GraphMol/ScaffoldNetwork && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitScaffoldNetwork.so.1.2020.09.3 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../lib/libRDKitMolStandardize.so.1.2020.09.3 ../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.3 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../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl cd /construction/science/rdkit/.build/Code/GraphMol/ScaffoldNetwork && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitScaffoldNetwork.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitScaffoldNetwork.so.1 CMakeFiles/CMakeRelink.dir/libRDKitScaffoldNetwork.so /usr/bin/make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdScaffoldNetwork.so cd /construction/science/rdkit/.build/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt 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-pthread -ldl /usr/bin/make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitMolEnumerator.so cd /construction/science/rdkit/.build/Code/GraphMol/MolEnumerator && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitMolEnumerator.so.1.2020.09.3 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../lib/libRDKitChemReactions.so.1.2020.09.3 ../../../lib/libRDKitChemTransforms.so.1.2020.09.3 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../../../lib/libRDKitRDGeometryLib.so.1.2020.09.3 ../../../lib/libRDKitRingDecomposerLib.so.1.2020.09.3 ../../../lib/libRDKitDataStructs.so.1.2020.09.3 ../../../lib/libRDKitRDGeneral.so.1.2020.09.3 -pthread -ldl /usr/local/lib/libboost_serialization.so cd /construction/science/rdkit/.build/Code/GraphMol/MolEnumerator && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitMolEnumerator.so.1.2020.09.3 CMakeFiles/CMakeRelink.dir/libRDKitMolEnumerator.so.1 CMakeFiles/CMakeRelink.dir/libRDKitMolEnumerator.so /usr/bin/make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdMolEnumerator.so cd /construction/science/rdkit/.build/Code/GraphMol/MolEnumerator/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing 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/construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolDraw2D/DrawTextJS.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolDraw2D.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolDraw2D.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolDraw2D.so -- Up-to-date: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolDraw2D/DrawText.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolDraw2D/DrawTextFT.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolDraw2D/DrawTextFTSVG.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolDraw2D/DrawTextFTJS.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/Draw/rdMolDraw2D.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitFMCS.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitFMCS.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitFMCS.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/FMCS/FMCS.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/FMCS/Graph.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdFMCS.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolHash.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolHash.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolHash.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolHash/MolHash.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolHash/nmmolhash.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdMolHash.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMMPA.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMMPA.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMMPA.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MMPA/MMPA.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdMMPA.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitCIPLabeler.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitCIPLabeler.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitCIPLabeler.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/CIPLabeler/CIPLabeler.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdCIPLabeler.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitDeprotect.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitDeprotect.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitDeprotect.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/Deprotect/Deprotect.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdDeprotect.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitReducedGraphs.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitReducedGraphs.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitReducedGraphs.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdReducedGraphs.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitTrajectory.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitTrajectory.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitTrajectory.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/Trajectory/Snapshot.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/Trajectory/Trajectory.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitSubstructLibrary.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitSubstructLibrary.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitSubstructLibrary.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/SubstructLibrary/PatternFactory.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdSubstructLibrary.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitRGroupDecomposition.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitRGroupDecomposition.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitRGroupDecomposition.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdRGroupDecomposition.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolInterchange.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolInterchange.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolInterchange.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolInterchange/MolInterchange.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolInterchange/details.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdMolInterchange.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitSLNParse.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitSLNParse.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitSLNParse.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/SLNParse/SLNAttribs.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/SLNParse/SLNParse.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/SLNParse/SLNParseOps.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdSLNParse.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdchem.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdmolops.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdqueries.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdmolfiles.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdtrajectory.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolStandardize.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolStandardize.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolStandardize.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/MolStandardize.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/Metal.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/Normalize.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/Validate.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/Charge.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/Tautomer.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/Fragment.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/MolStandardize/rdMolStandardize.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitScaffoldNetwork.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitScaffoldNetwork.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitScaffoldNetwork.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolEnumerator.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolEnumerator.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitMolEnumerator.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/MolEnumerator/MolEnumerator.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdMolEnumerator.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitAbbreviations.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitAbbreviations.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitAbbreviations.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/GraphMol/Abbreviations/Abbreviations.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdAbbreviations.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Query/AndQuery.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Query/EqualityQuery.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Query/GreaterEqualQuery.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Query/GreaterQuery.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Query/LessEqualQuery.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Query/LessQuery.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Query/NullQueryAlgebra.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Query/OrQuery.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Query/Query.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Query/QueryObjects.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Query/RangeQuery.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Query/SetQuery.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Query/XOrQuery.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/Features/Feature.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/DataManip/MetricMatrixCalc/MetricFuncs.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitSimDivPickers.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitSimDivPickers.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitSimDivPickers.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/SimDivPickers/DistPicker.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/SimDivPickers/LeaderPicker.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/SimDivPickers/HierarchicalClusterPicker.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/SimDivPickers/MaxMinPicker.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/SimDivFilters/rdSimDivPickers.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKithc.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKithc.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKithc.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/ML/Cluster/Clustering.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitInfoTheory.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitInfoTheory.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitInfoTheory.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/ML/InfoTheory/rdInfoTheory.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/ML/Data/cQuantize.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitChemicalFeatures.so.1.2020.09.3 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitChemicalFeatures.so.1 -- Installing: /construction/science/rdkit/stage/usr/local/lib/libRDKitChemicalFeatures.so -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/ChemicalFeatures/ChemicalFeature.h -- Installing: /construction/science/rdkit/stage/usr/local/include/rdkit/ChemicalFeatures/FreeChemicalFeature.h -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/Chem/rdChemicalFeatures.so -- Installing: /construction/science/rdkit/stage/usr/local/lib/python3.7/site-packages/rdkit/RDPaths.py ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/libRDKitChemReactions.so.1.2020.09.3 is linked to /usr/local/lib/libicudata.so.68 from devel/icu but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libicudata.so:devel/icu Error: /usr/local/lib/libRDKitChemReactions.so.1.2020.09.3 is linked to /usr/local/lib/libicui18n.so.68 from devel/icu but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libicui18n.so:devel/icu Error: /usr/local/lib/libRDKitChemReactions.so.1.2020.09.3 is linked to /usr/local/lib/libicuuc.so.68 from devel/icu but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libicuuc.so:devel/icu Error: /usr/local/lib/libRDKitMolDraw2D.so.1.2020.09.3 is linked to /usr/local/lib/libpng16.so.16 from graphics/png but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libpng16.so:graphics/png Error: /usr/local/lib/libRDKitRDBoost.so.1.2020.09.3 is linked to /usr/local/lib/libintl.so.8 from devel/gettext-runtime but it is not declared as a dependency Warning: you need USES+=gettext-runtime Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:01:05 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for rdkit-2020.09.3 file sizes/checksums [1663]: 0% file sizes/checksums [1663]: 6% file sizes/checksums [1663]: 12% file sizes/checksums [1663]: 18% file sizes/checksums [1663]: 24% file sizes/checksums [1663]: 30% file sizes/checksums [1663]: 36% file sizes/checksums [1663]: 42% file sizes/checksums [1663]: 48% file sizes/checksums [1663]: 54% file sizes/checksums [1663]: 60% file sizes/checksums [1663]: 66% file sizes/checksums [1663]: 72% file sizes/checksums [1663]: 78% file sizes/checksums [1663]: 84% file sizes/checksums [1663]: 90% file sizes/checksums [1663]: 96% file sizes/checksums [1663]: 100% packing files [1663]: 0% packing files [1663]: 6% packing files [1663]: 12% packing files [1663]: 18% packing files [1663]: 24% packing files [1663]: 30% packing files [1663]: 36% packing files [1663]: 42% packing files [1663]: 48% packing files [1663]: 54% packing files [1663]: 60% packing files [1663]: 66% packing files [1663]: 72% packing files [1663]: 78% packing files [1663]: 84% packing files [1663]: 90% packing files [1663]: 96% packing files [1663]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:01:50 TOTAL TIME 00:29:50