=> Building science/rdkit Started : Friday, 26 JUL 2019 at 08:37:48 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.6-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.6-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for rdkit-2018.09.3_2: DOCS=on: Build and/or install documentation PYTHON=on: Python bindings or support ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- PYTHON="/usr/local/bin/python3.6" 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 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/science/rdkit/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- SHLIB_VER=2018.09.3 PORTDOCS="" DOCS="" NO_DOCS="@comment " PYTHON="" NO_PYTHON="@comment " CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=5.6 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" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.6 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500601 OSVERSION=9999999 OSREL=5.6 _OSRELEASE=5.6-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> rdkit-2018.09.3_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> rdkit-2018.09.3_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of rdkit-2018.09.3_2 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by rdkit-2018.09.3_2 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by rdkit-2018.09.3_2 for building => SHA256 Checksum OK for rdkit-rdkit-Release_2018_09_3_GH0.tar.gz. => SHA256 Checksum OK for schrodinger-maeparser-1.0.0_GH0.tar.gz. => SHA256 Checksum OK for schrodinger-coordgenlibs-ede3191_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by rdkit-2018.09.3_2 for building ===> Extracting for rdkit-2018.09.3_2 => SHA256 Checksum OK for rdkit-rdkit-Release_2018_09_3_GH0.tar.gz. => SHA256 Checksum OK for schrodinger-maeparser-1.0.0_GH0.tar.gz. => SHA256 Checksum OK for schrodinger-coordgenlibs-ede3191_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for rdkit-2018.09.3_2 ===> Applying ports patches for rdkit-2018.09.3_2 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> rdkit-2018.09.3_2 depends on package: catch>0 - not found ===> Installing existing package /packages/All/catch-2.9.1.txz Installing catch-2.9.1... Extracting catch-2.9.1: .......... done ===> rdkit-2018.09.3_2 depends on package: catch>0 - found ===> Returning to build of rdkit-2018.09.3_2 ===> rdkit-2018.09.3_2 depends on executable: flex - found ===> rdkit-2018.09.3_2 depends on package: rapidjson>=0 - not found ===> Installing existing package /packages/All/rapidjson-1.1.0_5.txz Installing rapidjson-1.1.0_5... Extracting rapidjson-1.1.0_5: .......... done ===> rdkit-2018.09.3_2 depends on package: rapidjson>=0 - found ===> Returning to build of rdkit-2018.09.3_2 ===> rdkit-2018.09.3_2 depends on package: py36-numpy>0 - not found ===> Installing existing package /packages/All/py36-numpy-1.16.4,1.txz Installing py36-numpy-1.16.4,1... `-- Installing gcc8-8.3.0_2... | `-- Installing binutils-2.32_1,1... | | `-- Installing gettext-runtime-0.20.1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.20.1: .......... done | `-- Extracting binutils-2.32_1,1: .......... done | `-- Installing gmp-6.1.2_1... | `-- Extracting gmp-6.1.2_1: .......... done | `-- Installing mpc-1.1.0_2... | | `-- Installing mpfr-4.0.2... | | `-- Extracting mpfr-4.0.2: .......... done | `-- Extracting mpc-1.1.0_2: ......... done `-- Extracting gcc8-8.3.0_2: .......... done `-- Installing openblas-0.2.20_8,1... `-- Extracting openblas-0.2.20_8,1: ......... done `-- Installing py36-setuptools-41.0.1... | `-- Installing python36-3.6.9... | | `-- Installing expat-2.2.6_1... | | `-- Extracting expat-2.2.6_1: .......... done | | `-- Installing libffi-3.2.1_3... | | `-- Extracting libffi-3.2.1_3: .......... done | | `-- Installing libressl-2.9.2... | | `-- Extracting libressl-2.9.2: .......... done | | `-- Installing ncurses-6.1.20190525... | | `-- Extracting ncurses-6.1.20190525: .......... done | | `-- Installing readline-8.0.0... | | `-- Extracting readline-8.0.0: .......... done | `-- Extracting python36-3.6.9: .......... done `-- Extracting py36-setuptools-41.0.1: .......... done `-- Installing suitesparse-5.2.0_3... | `-- Installing lapack-3.5.0_7... | | `-- Installing blas-3.5.0_5... | | `-- Extracting blas-3.5.0_5: ....... done | `-- Extracting lapack-3.5.0_7: .......... done | `-- Installing metis-5.1.0_7... | `-- Extracting metis-5.1.0_7: .......... done `-- Extracting suitesparse-5.2.0_3: .......... done Extracting py36-numpy-1.16.4,1: .......... done Message from gcc8-8.3.0_2: 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. Message from python36-3.6.9: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== Message from metis-5.1.0_7: ===> 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 ===> rdkit-2018.09.3_2 depends on package: py36-numpy>0 - found ===> Returning to build of rdkit-2018.09.3_2 ===> rdkit-2018.09.3_2 depends on executable: bison - not found ===> Installing existing package /packages/All/bison-3.4.1,1.txz Installing bison-3.4.1,1... `-- Installing libtextstyle-0.20.1... `-- Extracting libtextstyle-0.20.1: .......... done `-- Installing m4-1.4.18_1,1... `-- Extracting m4-1.4.18_1,1: .......... done Extracting bison-3.4.1,1: .......... done ===> rdkit-2018.09.3_2 depends on executable: bison - found ===> Returning to build of rdkit-2018.09.3_2 ===> rdkit-2018.09.3_2 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.14.5.txz Installing cmake-3.14.5... `-- Installing curl-7.65.1_1... | `-- Installing ca_root_nss-3.45... | `-- Extracting ca_root_nss-3.45: ........ done | `-- Installing libnghttp2-1.39.1... | `-- Extracting libnghttp2-1.39.1: .......... done `-- Extracting curl-7.65.1_1: .......... done `-- Installing jsoncpp-1.8.1_6... `-- Extracting jsoncpp-1.8.1_6: .......... done `-- Installing libarchive-3.3.3_1,1... | `-- Installing liblz4-1.9.1,1... | `-- Extracting liblz4-1.9.1,1: .......... done | `-- Installing lzo2-2.10_1... | `-- Extracting lzo2-2.10_1: .......... done `-- Extracting libarchive-3.3.3_1,1: .......... done `-- Installing libuv-1.30.1... `-- Extracting libuv-1.30.1: .......... done `-- Installing rhash-1.3.5... `-- Extracting rhash-1.3.5: .......... done Extracting cmake-3.14.5: .......... done Message from ca_root_nss-3.45: ********************************* WARNING ********************************* 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. *********************************** NOTE ********************************** 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 *************************************************************************** ===> rdkit-2018.09.3_2 depends on file: /usr/local/bin/cmake - found ===> Returning to build of rdkit-2018.09.3_2 ===> rdkit-2018.09.3_2 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.3.7.txz Installing eigen-3.3.7... Extracting eigen-3.3.7: .......... done ===> rdkit-2018.09.3_2 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> Returning to build of rdkit-2018.09.3_2 ===> rdkit-2018.09.3_2 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> rdkit-2018.09.3_2 depends on shared library: libboost_system.so - not found ===> Installing existing package /packages/All/boost-libs-1.70.0_2.txz Installing boost-libs-1.70.0_2... `-- Installing icu-64.2,1... `-- Extracting icu-64.2,1: .......... done Extracting boost-libs-1.70.0_2: .......... done Message from boost-libs-1.70.0_2: You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> rdkit-2018.09.3_2 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so) ===> Returning to build of rdkit-2018.09.3_2 ===> rdkit-2018.09.3_2 depends on shared library: libboost_python36.so - not found ===> Installing existing package /packages/All/py36-boost-libs-1.70.0_2.txz Installing py36-boost-libs-1.70.0_2... Extracting py36-boost-libs-1.70.0_2: .......... done Message from py36-boost-libs-1.70.0_2: You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. You have built the Boost.Python library. You have to add the following options when building your own code: Compiler options: -I/usr/local/include/python3.6m -I/usr/local/include Linker options: -L/usr/local/lib/python3.6 -L/usr/local/lib -lboost_python -lpython3.6 ===> rdkit-2018.09.3_2 depends on shared library: libboost_python36.so - found (/usr/local/lib/libboost_python36.so) ===> Returning to build of rdkit-2018.09.3_2 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for rdkit-2018.09.3_2 ===> 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 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- Found Catch2 source in /usr/local CATCH: /usr/local/include/catch2 -- Found PythonInterp: /usr/local/bin/python3.6 (found version "3.6.9") -- Found PythonLibs: /usr/local/lib/libpython3.6m.so (found version "3.6.9") CMake Warning at /usr/local/share/cmake/Modules/FindBoost.cmake:1837 (message): No header defined for python-py36; skipping header check Call Stack (most recent call first): CMakeLists.txt:236 (find_package) Python Install directory /usr/local/lib/python3.6/site-packages PYTHON Py_ENABLE_SHARED: 1 PYTHON USING LINK LINE: -shared -lpthread -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 -- Boost version: 1.70.0 -- Found the following Boost libraries: -- serialization == Using strict rotor definition -- Found MAEParser source in /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/maeparser -- Found coordgenlibs source in /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs == Updating Filters.cpp from pains file == Done updating pains files -- Found RapidJSON source in /construction/science/rdkit/rdkit-Release_2018_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 -- Build files have been written to: /construction/science/rdkit/.build -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for rdkit-2018.09.3_2 /usr/local/bin/cmake -S/construction/science/rdkit/rdkit-Release_2018_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/catch/CMakeFiles/catch.dir/all --- /usr/bin/make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.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/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/catch/CMakeFiles/catch.dir/all --- --- External/catch/CMakeFiles/catch.dir/depend --- --- External/CoordGen/CMakeFiles/coordgen_support.dir/all --- --- External/CoordGen/CMakeFiles/coordgen_support.dir/depend --- --- External/INCHI-API/CMakeFiles/inchi_support.dir/all --- --- External/INCHI-API/CMakeFiles/inchi_support.dir/depend --- --- External/catch/CMakeFiles/catch.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/INCHI-API/CMakeFiles/inchi_support.dir/all --- Scanning dependencies of target inchi_support --- External/CoordGen/CMakeFiles/coordgen_support.dir/all --- Scanning dependencies of target coordgen_support --- External/catch/CMakeFiles/catch.dir/all --- Scanning dependencies of target catch /usr/bin/make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/build --- 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/build --- 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/build --- inchi_support --- cd /construction/science/rdkit/.build/External/INCHI-API && /usr/local/bin/cmake -E copy /construction/science/rdkit/rdkit-Release_2018_09_3/External/INCHI-API/python/noinchi.py /construction/science/rdkit/rdkit-Release_2018_09_3/rdkit/Chem/inchi.py --- External/catch/CMakeFiles/catch.dir/all --- [ 0%] Built target catch --- External/CoordGen/CMakeFiles/maeparser.dir/all --- --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/all --- --- Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/all --- --- External/CoordGen/CMakeFiles/maeparser.dir/all --- /usr/bin/make -f External/CoordGen/CMakeFiles/maeparser.dir/build.make External/CoordGen/CMakeFiles/maeparser.dir/depend --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/all --- /usr/bin/make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend --- Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/all --- /usr/bin/make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend --- External/CoordGen/CMakeFiles/coordgen_support.dir/all --- [ 0%] Built target coordgen_support --- Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/all --- --- Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/hc.dir/DependInfo.cmake --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/all --- --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/RDGeneral /construction/science/rdkit/.build/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake --- External/INCHI-API/CMakeFiles/inchi_support.dir/all --- [ 0%] Built target inchi_support --- External/CoordGen/CMakeFiles/maeparser.dir/all --- --- External/CoordGen/CMakeFiles/maeparser.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen /construction/science/rdkit/.build /construction/science/rdkit/.build/External/CoordGen /construction/science/rdkit/.build/External/CoordGen/CMakeFiles/maeparser.dir/DependInfo.cmake --- 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 --- --- Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o --- --- Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o --- [ 0%] 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 -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_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 -o CMakeFiles/hc.dir/hc.c.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ML/Cluster/Murtagh/hc.c --- Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o --- [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /construction/science/rdkit/.build/Code/ML/Cluster/Murtagh && /usr/bin/cc -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -Wno-deprecated -Wno-unused-function 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-pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/maeparser.dir/maeparser/MaeParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/maeparser/MaeParser.cpp --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/all --- Scanning dependencies of target RDGeneral /usr/bin/make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o --- [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/Invariant.cpp --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o --- [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/types.cpp --- Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o --- [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 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/construction/science/rdkit/.build/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/versions.cpp --- lib/libRDKitRDGeneral.so.1.2018.09.3 --- [ 2%] Linking CXX shared library 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/construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/RDGeneral /construction/science/rdkit/.build/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --- Code/RDBoost/CMakeFiles/RDBoost.dir/all --- --- Code/RDBoost/CMakeFiles/RDBoost.dir/depend --- --- Code/RDGeneral/CMakeFiles/testDict.dir/all --- --- Code/RDGeneral/CMakeFiles/testDict.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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/RDGeneral/CMakeFiles/testDict.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/RDGeneral /construction/science/rdkit/.build/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/RDGeneral/CMakeFiles/testDict.dir/all --- Scanning dependencies of target testDict /usr/bin/make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build --- Code/RDBoost/CMakeFiles/RDBoost.dir/all --- Scanning dependencies of target RDBoost /usr/bin/make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build --- Code/RDGeneral/CMakeFiles/testDict.dir/all --- --- Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o --- [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testDict.dir/testDict.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/testDict.cpp --- Code/RDBoost/CMakeFiles/RDBoost.dir/all --- --- Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o --- [ 3%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o cd /construction/science/rdkit/.build/Code/RDBoost && /usr/bin/c++ -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/Wrap.cpp --- Code/RDGeneral/CMakeFiles/testRDValue.dir/all --- Scanning dependencies of target testRDValue /usr/bin/make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build --- Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o --- [ 4%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/testRDValue.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 --- [ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/BitVect.cpp --- Code/RDGeneral/CMakeFiles/testRDValue.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/testRDValue.cpp:5: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/BitVect.cpp:14: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o --- [ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseBitVect.cpp In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseBitVect.cpp:15: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- External/CoordGen/CMakeFiles/maeparser.dir/all --- --- lib/libRDKitmaeparser.so.1.2018.09.3 --- [ 4%] Linking CXX shared library ../../lib/libRDKitmaeparser.so cd /construction/science/rdkit/.build/External/CoordGen && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/maeparser.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitmaeparser.so.1 -o ../../lib/libRDKitmaeparser.so.1.2018.09.3 CMakeFiles/maeparser.dir/maeparser/Buffer.cpp.o CMakeFiles/maeparser.dir/maeparser/MaeBlock.cpp.o CMakeFiles/maeparser.dir/maeparser/MaeParser.cpp.o CMakeFiles/maeparser.dir/maeparser/Reader.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../lib/libRDKitmaeparser.so.1 ../../lib/libRDKitmaeparser.so [ 4%] Built target maeparser --- Code/Numerics/CMakeFiles/testMatrices.dir/all --- /usr/bin/make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend --- Code/Numerics/CMakeFiles/testMatrices.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/Numerics /construction/science/rdkit/.build/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake Scanning dependencies of target testMatrices /usr/bin/make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build --- Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o --- [ 5%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o cd /construction/science/rdkit/.build/Code/Numerics && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics/testMatrices.cpp --- Code/RDBoost/CMakeFiles/RDBoost.dir/all --- --- lib/libRDKitRDBoost.so.1.2018.09.3 --- [ 6%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/RDBoost.dir/Wrap.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../lib/libRDKitRDGeneral.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so -pthread cd /construction/science/rdkit/.build/Code/RDBoost && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2018.09.3 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so [ 6%] Built target RDBoost --- 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/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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o --- --- Code/RDGeneral/CMakeFiles/testRDValue.dir/all --- --- Code/RDGeneral/testRDValue --- --- Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/all --- [ 6%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o cd /construction/science/rdkit/.build/Code/Numerics/EigenSolvers && /usr/bin/c++ -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp --- Code/RDGeneral/CMakeFiles/testRDValue.dir/all --- [ 6%] Linking CXX executable testRDValue cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 6%] Built target testRDValue --- Code/Catalogs/CMakeFiles/Catalogs.dir/all --- /usr/bin/make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/DataStructs/CMakeFiles/DataStructs.dir/all --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o --- [ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/ExplicitBitVect.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 --- [ 7%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o cd /construction/science/rdkit/.build/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/ExplicitBitVect.cpp:15: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/RDGeneral/CMakeFiles/testDict.dir/all --- --- Code/RDGeneral/testDict --- [ 7%] Linking CXX executable testDict cd /construction/science/rdkit/.build/Code/RDGeneral && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testDict.dir/testDict.cpp.o -o testDict -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 7%] Built target testDict --- Code/Query/CMakeFiles/testQuery.dir/all --- /usr/bin/make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend --- Code/Query/CMakeFiles/testQuery.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Query /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/Query /construction/science/rdkit/.build/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake Scanning dependencies of target testQuery /usr/bin/make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build --- Code/Query/CMakeFiles/testQuery.dir/test.cpp.o --- [ 7%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o cd /construction/science/rdkit/.build/Code/Query && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testQuery.dir/test.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Query/test.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o --- [ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Utils.cpp --- Code/Numerics/CMakeFiles/testMatrices.dir/all --- --- Code/Numerics/testMatrices --- [ 7%] Linking CXX executable testMatrices cd /construction/science/rdkit/.build/Code/Numerics && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 7%] Built target testMatrices --- Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/all --- /usr/bin/make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend --- Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataManip/MetricMatrixCalc /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/DataManip/MetricMatrixCalc /construction/science/rdkit/.build/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake Scanning dependencies of target testMatCalc /usr/bin/make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build --- Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o --- [ 7%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o cd /construction/science/rdkit/.build/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp --- Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/all --- --- lib/libRDKitEigenSolvers.so.1.2018.09.3 --- [ 7%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/Numerics/EigenSolvers && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so [ 7%] Built target EigenSolvers --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/all --- /usr/bin/make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 Scanning dependencies of target SimDivPickers /usr/bin/make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o --- [ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o cd /construction/science/rdkit/.build/Code/SimDivPickers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/SimDivPickers/DistPicker.cpp --- Code/Catalogs/CMakeFiles/Catalogs.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.cpp:13: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/all --- --- Code/DataManip/MetricMatrixCalc/testMatCalc --- [ 7%] Linking CXX executable testMatCalc cd /construction/science/rdkit/.build/Code/DataManip/MetricMatrixCalc && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 7%] Built target testMatCalc --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/all --- --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o --- [ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o cd /construction/science/rdkit/.build/Code/SimDivPickers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/SimDivPickers/MaxMinPicker.cpp --- Code/Catalogs/CMakeFiles/Catalogs.dir/all --- --- Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o --- [ 7%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o cd /construction/science/rdkit/.build/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/CatalogParams.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o --- [ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/base64.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o --- [ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/BitOps.cpp --- Code/Catalogs/CMakeFiles/Catalogs.dir/all --- --- 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++ -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/CatalogEntry.cpp --- lib/libRDKitCatalogs.so.1.2018.09.3 --- [ 7%] 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 -std=c++11 -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.1.2018.09.3 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.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/Catalogs && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so [ 8%] Built target Catalogs --- External/CoordGen/CMakeFiles/coordgenlib.dir/all --- /usr/bin/make -f External/CoordGen/CMakeFiles/coordgenlib.dir/build.make External/CoordGen/CMakeFiles/coordgenlib.dir/depend --- External/CoordGen/CMakeFiles/coordgenlib.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen /construction/science/rdkit/.build /construction/science/rdkit/.build/External/CoordGen /construction/science/rdkit/.build/External/CoordGen/CMakeFiles/coordgenlib.dir/DependInfo.cmake Scanning dependencies of target coordgenlib /usr/bin/make -f External/CoordGen/CMakeFiles/coordgenlib.dir/build.make External/CoordGen/CMakeFiles/coordgenlib.dir/build --- External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenFragmentBuilder.cpp.o --- [ 8%] Building CXX object External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenFragmentBuilder.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dcoordgenlib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenFragmentBuilder.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs/CoordgenFragmentBuilder.cpp --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/all --- --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o --- [ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /construction/science/rdkit/.build/Code/SimDivPickers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/SimDivPickers/HierarchicalClusterPicker.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/BitOps.cpp:16: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/Query/CMakeFiles/testQuery.dir/all --- --- Code/Query/testQuery --- [ 8%] Linking CXX executable testQuery cd /construction/science/rdkit/.build/Code/Query && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testQuery.dir/test.cpp.o -o testQuery -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 8%] Built target testQuery --- 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/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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o --- [ 8%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /construction/science/rdkit/.build/Code/RDBoost/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/Wrap/RDBase.cpp --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o --- [ 8%] 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++ -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ML/Cluster/Murtagh/Clustering.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o --- [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/DiscreteDistMat.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o --- [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/DiscreteValueVect.cpp --- Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/all --- --- lib/libRDKitSimDivPickers.so.1.2018.09.3 --- [ 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 -std=c++11 -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.1.2018.09.3 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.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/SimDivPickers && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2018.09.3 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so [ 9%] Built target SimDivPickers --- Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/all --- /usr/bin/make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend --- Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/SimDivPickers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/SimDivPickers /construction/science/rdkit/.build/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake Scanning dependencies of target testSimDivPickers /usr/bin/make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build --- Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o --- [ 9%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /construction/science/rdkit/.build/Code/SimDivPickers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/SimDivPickers/testPickers.cpp --- External/CoordGen/CMakeFiles/coordgenlib.dir/all --- --- External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenFragmenter.cpp.o --- [ 10%] Building CXX object External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenFragmenter.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dcoordgenlib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenFragmenter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs/CoordgenFragmenter.cpp--- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/DiscreteValueVect.cpp:13: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- External/CoordGen/CMakeFiles/coordgenlib.dir/all --- --- External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenMacrocycleBuilder.cpp.o --- [ 10%] Building CXX object External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenMacrocycleBuilder.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dcoordgenlib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenMacrocycleBuilder.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs/CoordgenMacrocycleBuilder.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o --- [ 10%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/FPBReader.cpp --- Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/all --- --- rdkit/ML/Cluster/Clustering.so --- [ 10%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 10%] Built target Clustering --- External/CoordGen/CMakeFiles/coordgenlib.dir/all --- --- External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenMinimizer.cpp.o --- [ 10%] Building CXX object External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenMinimizer.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dcoordgenlib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenMinimizer.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs/CoordgenMinimizer.cpp --- Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/all --- --- Code/SimDivPickers/testSimDivPickers --- [ 10%] Linking CXX executable testSimDivPickers cd /construction/science/rdkit/.build/Code/SimDivPickers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitSimDivPickers.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../lib/libRDKithc.so.1.2018.09.3 [ 10%] Built target testSimDivPickers --- External/CoordGen/CMakeFiles/coordgenlib.dir/all --- --- External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizer.cpp.o --- [ 10%] Building CXX object External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizer.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dcoordgenlib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizer.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs/sketcherMinimizer.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/FPBReader.cpp:19: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- External/CoordGen/CMakeFiles/coordgenlib.dir/all --- --- External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerAtom.cpp.o --- [ 10%] Building CXX object External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerAtom.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dcoordgenlib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerAtom.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs/sketcherMinimizerAtom.cpp --- External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerBond.cpp.o --- [ 10%] Building CXX object External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerBond.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dcoordgenlib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerBond.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs/sketcherMinimizerBond.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- --- Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o --- [ 11%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/MultiFPBReader.cpp --- External/CoordGen/CMakeFiles/coordgenlib.dir/all --- --- External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerFragment.cpp.o --- [ 11%] Building CXX object External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerFragment.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dcoordgenlib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerFragment.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs/sketcherMinimizerFragment.cpp --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/local/include/boost/python/extract.hpp: In static member function 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::__cxx11::list >; DerivedPolicies = boost::python::detail::final_list_derived_policies >, true>; bool NoProxy = true; bool NoSlice = false; Data = int; Index = long unsigned int; Key = int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& x +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::__cxx11::list >; DerivedPolicies = boost::python::detail::final_list_derived_policies >, false>; bool NoProxy = false; bool NoSlice = false; Data = int; Index = long unsigned int; Key = int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& x +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- External/CoordGen/CMakeFiles/coordgenlib.dir/all --- --- External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerMarchingSquares.cpp.o --- [ 12%] Building CXX object External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerMarchingSquares.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dcoordgenlib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerMarchingSquares.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs/sketcherMinimizerMarchingSquares.cpp --- External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerMolecule.cpp.o --- [ 12%] Building CXX object External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerMolecule.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dcoordgenlib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerMolecule.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs/sketcherMinimizerMolecule.cpp --- External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerResidue.cpp.o --- [ 12%] Building CXX object External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerResidue.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dcoordgenlib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerResidue.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs/sketcherMinimizerResidue.cpp --- Code/DataStructs/CMakeFiles/DataStructs.dir/all --- --- lib/libRDKitDataStructs.so.1.2018.09.3 --- [ 12%] 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 -std=c++11 -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.1.2018.09.3 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.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/DataStructs && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so [ 12%] Built target DataStructs --- Code/DataStructs/CMakeFiles/testDataStructs.dir/all --- /usr/bin/make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend --- Code/DataStructs/CMakeFiles/testDataStructs.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/DataStructs /construction/science/rdkit/.build/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake Scanning dependencies of target testDataStructs /usr/bin/make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build --- Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o --- [ 12%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/testDatastructs.cpp --- External/CoordGen/CMakeFiles/coordgenlib.dir/all --- --- External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerResidueInteraction.cpp.o --- [ 12%] Building CXX object External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerResidueInteraction.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dcoordgenlib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerResidueInteraction.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs/sketcherMinimizerResidueInteraction.cpp --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- /usr/local/include/boost/python/extract.hpp: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- External/CoordGen/CMakeFiles/coordgenlib.dir/all --- --- External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerRing.cpp.o --- [ 12%] Building CXX object External/CoordGen/CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerRing.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dcoordgenlib_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerRing.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/coordgenlibs/sketcherMinimizerRing.cpp --- Code/DataStructs/CMakeFiles/testFPB.dir/all --- /usr/bin/make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend --- Code/DataStructs/CMakeFiles/testFPB.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/DataStructs /construction/science/rdkit/.build/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake Scanning dependencies of target testFPB /usr/bin/make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build --- Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o --- [ 12%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/testFPB.cpp --- Code/DataStructs/CMakeFiles/testMultiFPB.dir/all --- /usr/bin/make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend --- Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/DataStructs /construction/science/rdkit/.build/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake Scanning dependencies of target testMultiFPB /usr/bin/make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build --- Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o --- [ 12%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs && /usr/bin/c++ -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/testMultiFPB.cpp --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, true> >, long unsigned int>; Data = int; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = int; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, true> >, long unsigned int>; Data = unsigned int; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = unsigned int; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, true> >, long unsigned int>; Data = double; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = double; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector, std::allocator > >; DerivedPolicies = boost::python::detail::final_vector_derived_policies, std::allocator > >, true>; ProxyHandler = boost::python::detail::no_proxy_helper, std::allocator > >, boost::python::detail::final_vector_derived_policies, std::allocator > >, true>, boost::python::detail::container_element, std::allocator > >, long unsigned int, boost::python::detail::final_vector_derived_policies, std::allocator > >, true> >, long unsigned int>; Data = std::__cxx11::basic_string; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector, std::allocator > >; DerivedPolicies = boost::python::detail::final_vector_derived_policies, std::allocator > >, false>; ProxyHandler = boost::python::detail::no_proxy_helper, std::allocator > >, boost::python::detail::final_vector_derived_policies, std::allocator > >, false>, boost::python::detail::container_element, std::allocator > >, long unsigned int, boost::python::detail::final_vector_derived_policies, std::allocator > >, false> >, long unsigned int>; Data = std::__cxx11::basic_string; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector, std::allocator > >; DerivedPolicies = boost::python::detail::final_vector_derived_policies, std::allocator > >, true>; ProxyHandler = boost::python::detail::no_proxy_helper, std::allocator > >, boost::python::detail::final_vector_derived_policies, std::allocator > >, true>, boost::python::detail::container_element, std::allocator > >, long unsigned int, boost::python::detail::final_vector_derived_policies, std::allocator > >, true> >, long unsigned int>; Data = std::vector; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector, std::allocator > >; DerivedPolicies = boost::python::detail::final_vector_derived_policies, std::allocator > >, false>; ProxyHandler = boost::python::detail::proxy_helper, std::allocator > >, boost::python::detail::final_vector_derived_policies, std::allocator > >, false>, boost::python::detail::container_element, std::allocator > >, long unsigned int, boost::python::detail::final_vector_derived_policies, std::allocator > >, false> >, long unsigned int>; Data = std::vector; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector, std::allocator > >; DerivedPolicies = boost::python::detail::final_vector_derived_policies, std::allocator > >, true>; ProxyHandler = boost::python::detail::no_proxy_helper, std::allocator > >, boost::python::detail::final_vector_derived_policies, std::allocator > >, true>, boost::python::detail::container_element, std::allocator > >, long unsigned int, boost::python::detail::final_vector_derived_policies, std::allocator > >, true> >, long unsigned int>; Data = std::vector; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector, std::allocator > >; DerivedPolicies = boost::python::detail::final_vector_derived_policies, std::allocator > >, false>; ProxyHandler = boost::python::detail::proxy_helper, std::allocator > >, boost::python::detail::final_vector_derived_policies, std::allocator > >, false>, boost::python::detail::container_element, std::allocator > >, long unsigned int, boost::python::detail::final_vector_derived_policies, std::allocator > >, false> >, long unsigned int>; Data = std::vector; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector, std::allocator > >; DerivedPolicies = boost::python::detail::final_vector_derived_policies, std::allocator > >, true>; ProxyHandler = boost::python::detail::no_proxy_helper, std::allocator > >, boost::python::detail::final_vector_derived_policies, std::allocator > >, true>, boost::python::detail::container_element, std::allocator > >, long unsigned int, boost::python::detail::final_vector_derived_policies, std::allocator > >, true> >, long unsigned int>; Data = std::vector; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- External/CoordGen/CMakeFiles/coordgenlib.dir/all --- --- lib/libRDKitcoordgenlib.so.1.2018.09.3 --- [ 12%] Linking CXX shared library ../../lib/libRDKitcoordgenlib.so cd /construction/science/rdkit/.build/External/CoordGen && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/coordgenlib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitcoordgenlib.so.1 -o ../../lib/libRDKitcoordgenlib.so.1.2018.09.3 CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenFragmentBuilder.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenFragmenter.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenMacrocycleBuilder.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenMinimizer.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizer.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerAtom.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerBond.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerFragment.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerMarchingSquares.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerMolecule.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerResidue.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerResidueInteraction.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerRing.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitmaeparser.so.1.2018.09.3 cd /construction/science/rdkit/.build/External/CoordGen && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../lib/libRDKitcoordgenlib.so.1 ../../lib/libRDKitcoordgenlib.so [ 12%] Built target coordgenlib --- 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/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector, std::allocator > >; DerivedPolicies = boost::python::detail::final_vector_derived_policies, std::allocator > >, false>; ProxyHandler = boost::python::detail::proxy_helper, std::allocator > >, boost::python::detail::final_vector_derived_policies, std::allocator > >, false>, boost::python::detail::container_element, std::allocator > >, long unsigned int, boost::python::detail::final_vector_derived_policies, std::allocator > >, false> >, long unsigned int>; Data = std::vector; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::__cxx11::list >; DerivedPolicies = boost::python::detail::final_list_derived_policies >, true>; ProxyHandler = boost::python::detail::no_proxy_helper >, boost::python::detail::final_list_derived_policies >, true>, boost::python::detail::container_element >, long unsigned int, boost::python::detail::final_list_derived_policies >, true> >, long unsigned int>; Data = int; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/DataStructs/CMakeFiles/testDataStructs.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/testDatastructs.cpp:26: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::__cxx11::list >; DerivedPolicies = boost::python::detail::final_list_derived_policies >, false>; ProxyHandler = boost::python::detail::no_proxy_helper >, boost::python::detail::final_list_derived_policies >, false>, boost::python::detail::container_element >, long unsigned int, boost::python::detail::final_list_derived_policies >, false> >, long unsigned int>; Data = int; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::__cxx11::list, std::allocator > >; DerivedPolicies = boost::python::detail::final_list_derived_policies, std::allocator > >, true>; ProxyHandler = boost::python::detail::no_proxy_helper, std::allocator > >, boost::python::detail::final_list_derived_policies, std::allocator > >, true>, boost::python::detail::container_element, std::allocator > >, long unsigned int, boost::python::detail::final_list_derived_policies, std::allocator > >, true> >, long unsigned int>; Data = std::vector; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::__cxx11::list, std::allocator > >; DerivedPolicies = boost::python::detail::final_list_derived_policies, std::allocator > >, false>; ProxyHandler = boost::python::detail::proxy_helper, std::allocator > >, boost::python::detail::final_list_derived_policies, std::allocator > >, false>, boost::python::detail::container_element, std::allocator > >, long unsigned int, boost::python::detail::final_list_derived_policies, std::allocator > >, false> >, long unsigned int>; Data = std::vector; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- 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 --- [ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/DataStructs.cpp --- Code/DataStructs/CMakeFiles/testFPB.dir/all --- --- Code/DataStructs/testFPB --- [ 13%] Linking CXX executable testFPB cd /construction/science/rdkit/.build/Code/DataStructs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 13%] Built target testFPB --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- /usr/bin/make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 Scanning dependencies of target RDGeometryLib /usr/bin/make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o --- [ 13%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o cd /construction/science/rdkit/.build/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/point.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/DataStructs.cpp:17: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all --- --- rdkit/rdBase.so --- [ 14%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 14%] Built target rdBase --- 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/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o --- --- Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/all --- --- Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- [ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/DiscreteValueVect.cpp --- Code/DataStructs/CMakeFiles/testMultiFPB.dir/all --- --- Code/DataStructs/testMultiFPB --- [ 14%] Linking CXX executable testMultiFPB cd /construction/science/rdkit/.build/Code/DataStructs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 14%] Built target testMultiFPB --- 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/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/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/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o --- [ 14%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o cd /construction/science/rdkit/.build/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp --- 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/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o --- [ 14%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /construction/science/rdkit/.build/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp --- Code/DataStructs/CMakeFiles/testDataStructs.dir/all --- --- Code/DataStructs/testDataStructs --- [ 14%] Linking CXX executable testDataStructs cd /construction/science/rdkit/.build/Code/DataStructs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 14%] Built target testDataStructs --- 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/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 14%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /construction/science/rdkit/.build/Code/ML/InfoTheory && /usr/bin/c++ -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ML/InfoTheory/InfoBitRanker.cpp --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o --- [ 14%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o cd /construction/science/rdkit/.build/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/Transform2D.cpp --- Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/all --- --- lib/libRDKitInfoTheory.so.1.2018.09.3 --- [ 14%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o --- [ 14%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o --- Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/all --- cd /construction/science/rdkit/.build/Code/ML/InfoTheory && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2018.09.3 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- cd /construction/science/rdkit/.build/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/Transform3D.cpp --- Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/all --- [ 14%] Built target InfoTheory --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o --- [ 14%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o cd /construction/science/rdkit/.build/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/UniformGrid3D.cpp In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/UniformGrid3D.cpp:13: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:12: /usr/local/include/boost/python/extract.hpp: In function 'double RDDataManip::EuclideanDistanceMetric(const T1&, const T2&, unsigned int) [with T1 = PySequenceHolder; T2 = PySequenceHolder]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'PyObject* RDDataManip::getEuclideanDistMat(boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o --- [ 15%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o cd /construction/science/rdkit/.build/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/GridUtils.cpp --- Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/all --- /usr/local/include/boost/python/extract.hpp: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = SparseBitVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In member function 'void RDDataManip::MetricMatrixCalc::calcMetricMatrix(const vectType&, unsigned int, unsigned int, double*) [with vectType = PySequenceHolder; entryType = ExplicitBitVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o --- [ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/SparseIntVect.cpp --- Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/all --- /usr/local/include/boost/python/extract.hpp: In function 'PyObject* RDDataManip::getTanimotoDistMat(boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'PyObject* RDDataManip::getTanimotoSimMat(boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- rdkit/DataManip/Metric/rdMetricMatrixCalc.so --- [ 16%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 16%] Built target rdMetricMatrixCalc --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 16%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all --- --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o --- [ 17%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /construction/science/rdkit/.build/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:12: /usr/local/include/boost/python/extract.hpp: In member function 'RDKit::INT_VECT RDPickers::MaxMinPicker::lazyPick(T&, unsigned int, unsigned int, const INT_VECT&, int, double&) const [with T = RDPickers::pyobjFunctor]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'void RDPickers::{anonymous}::LazyMaxMinHelper(RDPickers::MaxMinPicker*, T, unsigned int, unsigned int, boost::python::api::object, int, RDKit::INT_VECT&, double&) [with T = RDPickers::pyobjFunctor]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'void RDPickers::{anonymous}::LazyMaxMinHelper(RDPickers::MaxMinPicker*, T, unsigned int, unsigned int, boost::python::api::object, int, RDKit::INT_VECT&, double&) [with T = RDPickers::pyBVFunctor]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'RDKit::INT_VECT RDPickers::MaxMinPicks(RDPickers::MaxMinPicker*, boost::python::api::object, int, int, boost::python::api::object, int)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o --- [ 17%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o cd /construction/science/rdkit/.build/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp --- Code/Geometry/CMakeFiles/RDGeometryLib.dir/all --- --- lib/libRDKitRDGeometryLib.so.1.2018.09.3 --- [ 17%] 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 -std=c++11 -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.1.2018.09.3 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.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/Geometry && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so [ 17%] Built target RDGeometryLib --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 17%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /construction/science/rdkit/.build/Code/ML/Data && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ML/Data/cQuantize.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/SparseIntVect.cpp:19: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp:12: /usr/local/include/boost/python/extract.hpp: In function 'void RDInfoTheory::SetMaskBits(RDInfoTheory::InfoBitRanker*, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'void RDInfoTheory::SetBiasList(RDInfoTheory::InfoBitRanker*, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o --- [ 17%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o --- [ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/wrap_SparseBV.cpp --- Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all --- --- rdkit/SimDivFilters/rdSimDivPickers.so --- [ 17%] 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 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.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.1.2018.09.3 ../../../lib/libRDKithc.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 17%] Built target rdSimDivPickers --- Code/Geometry/CMakeFiles/testTransforms.dir/all --- /usr/bin/make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend --- Code/Geometry/CMakeFiles/testTransforms.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/Geometry /construction/science/rdkit/.build/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake Scanning dependencies of target testTransforms /usr/bin/make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build --- Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o --- [ 17%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /construction/science/rdkit/.build/Code/Geometry && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/testTransforms.cpp --- Code/ML/Data/CMakeFiles/cQuantize.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/Wrap.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ML/Data/cQuantize.cpp:12: /usr/local/include/boost/python/extract.hpp: In function 'boost::python::tuple cQuantize_RecurseOnBounds(boost::python::api::object, boost::python::list, int, boost::python::list, boost::python::api::object, int)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- rdkit/ML/Data/cQuantize.so --- [ 17%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 17%] Built target cQuantize --- Code/Geometry/CMakeFiles/testGrid.dir/all --- /usr/bin/make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend --- Code/Geometry/CMakeFiles/testGrid.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/Geometry /construction/science/rdkit/.build/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake Scanning dependencies of target testGrid /usr/bin/make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build --- Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o --- [ 17%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o cd /construction/science/rdkit/.build/Code/Geometry && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/testGrid.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/SparseIntVect.cpp:11: /usr/local/include/boost/python/extract.hpp: In function 'void {anonymous}::pyUpdateFromSequence(RDKit::SparseIntVect&, boost::python::api::object&) [with IndexType = int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp:11: /usr/local/include/boost/python/extract.hpp: In function 'void RDInfoTheory::setBitList(RDInfoTheory::BitCorrMatGenerator*, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::BulkTversky(const T&, boost::python::list, double, double, bool) [with T = RDKit::SparseIntVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::BulkTanimoto(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/Geometry/CMakeFiles/testTransforms.dir/all --- --- Code/Geometry/testTransforms --- [ 17%] Linking CXX executable testTransforms cd /construction/science/rdkit/.build/Code/Geometry && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/all --- --- Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o --- [ 18%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp --- Code/Geometry/CMakeFiles/testTransforms.dir/all --- [ 18%] Built target testTransforms --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- /usr/local/include/boost/python/extract.hpp: In function 'void {anonymous}::pyUpdateFromSequence(RDKit::SparseIntVect&, boost::python::api::object&) [with IndexType = long int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::BulkTversky(const T&, boost::python::list, double, double, bool) [with T = RDKit::SparseIntVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::BulkTanimoto(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/all --- 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 --- [ 18%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /construction/science/rdkit/.build/Code/Geometry/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/Wrap/Point.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- /usr/local/include/boost/python/extract.hpp: In function 'void {anonymous}::pyUpdateFromSequence(RDKit::SparseIntVect&, boost::python::api::object&) [with IndexType = unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::BulkTversky(const T&, boost::python::list, double, double, bool) [with T = RDKit::SparseIntVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::BulkTanimoto(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'void {anonymous}::pyUpdateFromSequence(RDKit::SparseIntVect&, boost::python::api::object&) [with IndexType = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::BulkTversky(const T&, boost::python::list, double, double, bool) [with T = RDKit::SparseIntVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::BulkTanimoto(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/Wrap.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/wrap_SparseBV.cpp:11: /usr/local/include/boost/python/extract.hpp: In function 'void SetBitsFromList(T*, boost::python::api::object) [with T = SparseBitVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'void UnSetBitsFromList(T*, boost::python::api::object) [with T = SparseBitVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o --- [ 18%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp --- Code/Geometry/CMakeFiles/testGrid.dir/all --- --- Code/Geometry/testGrid --- [ 18%] Linking CXX executable testGrid cd /construction/science/rdkit/.build/Code/Geometry && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 18%] Built target testGrid --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 18%] 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 -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics/Alignment/AlignPoints.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o --- [ 18%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/wrap_BitOps.cpp --- Code/Numerics/Alignment/CMakeFiles/Alignment.dir/all --- --- lib/libRDKitAlignment.so.1.2018.09.3 --- [ 18%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/Numerics/Alignment && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so [ 18%] 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/all --- --- rdkit/ML/InfoTheory/rdInfoTheory.so --- [ 18%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 18%] Built target rdInfoTheory --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 19%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /construction/science/rdkit/.build/Code/ChemicalFeatures && /usr/bin/c++ -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ChemicalFeatures/FreeChemicalFeature.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 --- [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Atom.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/Wrap.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp:11: /usr/local/include/boost/python/extract.hpp: In function 'void UnSetBitsFromList(T*, boost::python::api::object) [with T = ExplicitBitVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'void SetBitsFromList(T*, boost::python::api::object) [with T = ExplicitBitVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o --- [ 21%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/wrap_FPB.cpp --- Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ChemicalFeatures/FreeChemicalFeature.cpp:12: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- lib/libRDKitChemicalFeatures.so.1.2018.09.3 --- [ 21%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/ChemicalFeatures && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2018.09.3 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so [ 21%] Built target ChemicalFeatures --- Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/all --- /usr/bin/make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend --- Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics/Alignment /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/Numerics/Alignment /construction/science/rdkit/.build/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake Scanning dependencies of target testAlignment /usr/bin/make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build --- Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o --- [ 21%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /construction/science/rdkit/.build/Code/Numerics/Alignment && /usr/bin/c++ -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics/Alignment/testAlignment.cpp --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/Wrap/Point.cpp:11: /usr/local/include/boost/python/extract.hpp: In static member function 'static void {anonymous}::PointND_pickle_suite::setstate(RDGeom::PointND&, boost::python::tuple)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o --- [ 21%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o cd /construction/science/rdkit/.build/Code/Geometry/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/Wrap/UniformGrid3D.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/wrap_BitOps.cpp:11: /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list BulkWrapper(const T&, boost::python::api::object, double, double, double (*)(const T&, const T&, double, double), bool) [with T = SparseBitVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list BulkWrapper(const T&, boost::python::api::object, double (*)(const T&, const T&), bool) [with T = SparseBitVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/all --- --- Code/Numerics/Alignment/testAlignment --- [ 22%] Linking CXX executable testAlignment cd /construction/science/rdkit/.build/Code/Numerics/Alignment && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list BulkWrapper(const T&, boost::python::api::object, double (*)(const T&, const T&), bool) [with T = ExplicitBitVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/all --- [ 22%] Built target testAlignment --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- Code/GraphMol/CMakeFiles/GraphMol.dir/all --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o --- [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/QueryAtom.cpp --- Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/all --- 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 --- [ 22%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list BulkWrapper(const T&, boost::python::api::object, double, double, double (*)(const T&, const T&, double, double), bool) [with T = ExplicitBitVect]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o --- [ 22%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -DcDataStructs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/Wrap/wrap_Utils.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/all --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o --- [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/QueryBond.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o --- [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Bond.cpp --- Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:12: /usr/local/include/boost/python/extract.hpp: In function 'void RDNumeric::Alignments::GetPointsFromPythonSequence(boost::python::api::object&, RDGeom::Point3DConstPtrVect&)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'PyObject* RDNumeric::Alignments::AlignPointPairs(boost::python::api::object, boost::python::api::object, boost::python::api::object, bool, unsigned int)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- rdkit/Numerics/rdAlignment.so --- [ 22%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 22%] Built target rdAlignment --- Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/all --- /usr/bin/make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend --- Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ChemicalFeatures /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/ChemicalFeatures /construction/science/rdkit/.build/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake Scanning dependencies of target 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-mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ChemicalFeatures/testChemicalFeatures.cpp --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/all --- --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o --- [ 22%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o cd /construction/science/rdkit/.build/Code/Geometry/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/Wrap/rdGeometry.cpp --- Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all --- --- rdkit/DataStructs/cDataStructs.so --- [ 22%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 22%] Built target cDataStructs --- Code/GraphMol/CMakeFiles/GraphMol.dir/all --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o --- [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolOps.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o --- [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FindRings.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o --- [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ROMol.cpp --- Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/all --- --- Code/ChemicalFeatures/testChemicalFeatures --- [ 22%] Linking CXX executable testChemicalFeatures cd /construction/science/rdkit/.build/Code/ChemicalFeatures && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitChemicalFeatures.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 22%] Built target testChemicalFeatures --- Code/GraphMol/CMakeFiles/GraphMol.dir/all --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o --- [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RWMol.cpp --- Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/all --- --- rdkit/Geometry/rdGeometry.so --- [ 22%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 22%] Built target rdGeometry --- Code/GraphMol/CMakeFiles/GraphMol.dir/all --- --- Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o --- [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/PeriodicTable.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o --- [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/atomic_data.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o --- [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/QueryOps.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o --- [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolPickler.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o --- In file included from /usr/local/include/boost/graph/adjacency_list.hpp:223, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ROMol.h:27, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ROMol.cpp:17: /usr/local/include/boost/graph/detail/adjacency_list.hpp: In member function 'unsigned int RDKit::ROMol::addBond(RDKit::Bond*, bool)': /usr/local/include/boost/graph/detail/adjacency_list.hpp:2240:43: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] typename Config::edge_property_type p; ^ --- Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o --- [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Canon.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o --- [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/AtomIterators.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o --- In file included from /usr/local/include/boost/graph/adjacency_list.hpp:223, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ROMol.h:27, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RWMol.h:21, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RWMol.cpp:16: /usr/local/include/boost/graph/detail/adjacency_list.hpp: In member function 'unsigned int RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType)': /usr/local/include/boost/graph/detail/adjacency_list.hpp:2240:43: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] typename Config::edge_property_type p; ^ --- Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o --- [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/BondIterators.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolPickler.cpp:17: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o --- [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Aromaticity.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o --- [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolDiscriminators.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o --- [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ConjugHybrid.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o --- [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/AddHs.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o --- [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Matrices.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o --- [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Chirality.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o --- [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RingInfo.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o --- [ 25%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Conformer.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o --- [ 25%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Renumber.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o --- [ 25%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/AdjustQuery.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o --- [ 25%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD 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-DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StereoGroup.cpp --- Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o --- [ 25%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/new_canon.cpp --- lib/libRDKitGraphMol.so.1.2018.09.3 --- [ 25%] 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 -std=c++11 -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.1.2018.09.3 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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so [ 26%] 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/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 Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend --- Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/all --- /usr/bin/make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/all --- /usr/bin/make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend --- Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/all --- /usr/bin/make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/Substruct/CMakeFiles/SubstructMatch.dir/all --- --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend --- --- Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/all --- --- Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend --- --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/all --- --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/SmilesParse /construction/science/rdkit/.build/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/Subgraphs/CMakeFiles/Subgraphs.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/PartialCharges/CMakeFiles/PartialCharges.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 Scanning dependencies of target PartialCharges --- Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/all --- Scanning dependencies of target MolTransforms /usr/bin/make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/all --- /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 --- --- Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/all --- --- Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o --- --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/all --- [ 26%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/PartialCharges && /usr/bin/c++ -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/PartialCharges/GasteigerCharges.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++ -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolTransforms/MolTransforms.cpp --- Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/all --- Scanning dependencies of target Subgraphs /usr/bin/make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build --- Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o --- [ 26%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Subgraphs/Subgraphs.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 --- [ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Substruct && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Substruct/SubstructMatch.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- Scanning dependencies of target SmilesParse /usr/bin/make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o --- [ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/SmilesParse.cpp --- Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/all --- --- Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o --- [ 26%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Subgraphs/SubgraphUtils.cpp --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/all --- --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o --- [ 26%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/PartialCharges && /usr/bin/c++ -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/PartialCharges/GasteigerParams.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o --- [ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp --- Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/all --- --- lib/libRDKitSubgraphs.so.1.2018.09.3 --- [ 26%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Subgraphs && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so [ 26%] Built target Subgraphs --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o --- [ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/SmilesWrite.cpp --- Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/all --- --- lib/libRDKitPartialCharges.so.1.2018.09.3 --- [ 26%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/PartialCharges && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so [ 26%] Built target PartialCharges --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/all --- /usr/bin/make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 Scanning dependencies of target MolCatalog /usr/bin/make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build --- 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++ -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp --- Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/all --- --- lib/libRDKitMolTransforms.so.1.2018.09.3 --- [ 26%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MolTransforms && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so [ 26%] Built target MolTransforms --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/all --- --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o --- [ 26%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolCatalog && /usr/bin/c++ -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolCatalog/MolCatalogParams.cpp --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/all --- --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o --- [ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Substruct && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Substruct/SubstructUtils.cpp --- 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/Trajectory/CMakeFiles/Trajectory.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 Scanning dependencies of target Trajectory /usr/bin/make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build --- 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++ -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Trajectory/Trajectory.cpp --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/all --- --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp:14: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o --- [ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/SmartsWrite.cpp --- Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/all --- --- lib/libRDKitSubstructMatch.so.1.2018.09.3 --- [ 26%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Substruct && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so [ 26%] Built target SubstructMatch --- 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/MolInterchange/CMakeFiles/MolInterchange.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 26%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolInterchange && /usr/bin/c++ -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/rapidjson-1.1.0/include -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolInterchange/Parser.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o --- [ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp --- Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/all --- --- lib/libRDKitMolCatalog.so.1.2018.09.3 --- [ 26%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MolCatalog && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2018.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so [ 26%] Built target MolCatalog --- 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/SLNParse/CMakeFiles/SLNParse.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SLNParse /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/SLNParse /construction/science/rdkit/.build/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake 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++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SLNParse/SLNParse.cpp --- Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/all --- In file included from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolInterchange/Parser.cpp:26: /usr/local/include/rapidjson/document.h: In instantiation of 'void rapidjson::GenericValue::SetObjectRaw(rapidjson::GenericValue::Member*, rapidjson::SizeType, Allocator&) [with Encoding = rapidjson::UTF8<>; Allocator = rapidjson::MemoryPoolAllocator<>; rapidjson::GenericValue::Member = rapidjson::GenericMember, rapidjson::MemoryPoolAllocator<> >; rapidjson::SizeType = unsigned int]': /usr/local/include/rapidjson/document.h:2363:9: required from 'bool rapidjson::GenericDocument::EndObject(rapidjson::SizeType) [with Encoding = rapidjson::UTF8<>; Allocator = rapidjson::MemoryPoolAllocator<>; StackAllocator = rapidjson::CrtAllocator; rapidjson::SizeType = unsigned int]' /usr/local/include/rapidjson/reader.h:1736:18: required from 'rapidjson::GenericReader::IterativeParsingState rapidjson::GenericReader::Transit(rapidjson::GenericReader::IterativeParsingState, rapidjson::GenericReader::Token, rapidjson::GenericReader::IterativeParsingState, InputStream&, Handler&) [with unsigned int parseFlags = 0; InputStream = rapidjson::BasicIStreamWrapper >; Handler = rapidjson::GenericDocument >; SourceEncoding = rapidjson::UTF8<>; TargetEncoding = rapidjson::UTF8<>; StackAllocator = rapidjson::CrtAllocator]' /usr/local/include/rapidjson/reader.h:1832:58: required from 'rapidjson::ParseResult rapidjson::GenericReader::IterativeParse(InputStream&, Handler&) [with unsigned int parseFlags = 0; InputStream = rapidjson::BasicIStreamWrapper >; Handler = rapidjson::GenericDocument >; SourceEncoding = rapidjson::UTF8<>; TargetEncoding = rapidjson::UTF8<>; StackAllocator = rapidjson::CrtAllocator]' /usr/local/include/rapidjson/reader.h:487:46: required from 'rapidjson::ParseResult rapidjson::GenericReader::Parse(InputStream&, Handler&) [with unsigned int parseFlags = 0; InputStream = rapidjson::BasicIStreamWrapper >; Handler = rapidjson::GenericDocument >; SourceEncoding = rapidjson::UTF8<>; TargetEncoding = rapidjson::UTF8<>; StackAllocator = rapidjson::CrtAllocator]' /usr/local/include/rapidjson/document.h:2159:22: required from 'rapidjson::GenericDocument& rapidjson::GenericDocument::ParseStream(InputStream&) [with unsigned int parseFlags = 0; SourceEncoding = rapidjson::UTF8<>; InputStream = rapidjson::BasicIStreamWrapper >; Encoding = rapidjson::UTF8<>; Allocator = rapidjson::MemoryPoolAllocator<>; StackAllocator = rapidjson::CrtAllocator]' /usr/local/include/rapidjson/document.h:2185:70: required from 'rapidjson::GenericDocument& rapidjson::GenericDocument::ParseStream(InputStream&) [with InputStream = rapidjson::BasicIStreamWrapper >; Encoding = rapidjson::UTF8<>; Allocator = rapidjson::MemoryPoolAllocator<>; StackAllocator = rapidjson::CrtAllocator]' /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolInterchange/Parser.cpp:458:22: required from here /usr/local/include/rapidjson/document.h:1952:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'rapidjson::GenericValue >::Member' {aka 'struct rapidjson::GenericMember, rapidjson::MemoryPoolAllocator<> >'} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess] std::memcpy(m, members, count * sizeof(Member)); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolInterchange/Parser.cpp:26: /usr/local/include/rapidjson/document.h:71:8: note: 'rapidjson::GenericValue >::Member' {aka 'struct rapidjson::GenericMember, rapidjson::MemoryPoolAllocator<> >'} declared here struct GenericMember { ^~~~~~~~~~~~~ In file included from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolInterchange/Parser.cpp:26: /usr/local/include/rapidjson/document.h: In instantiation of 'void rapidjson::GenericValue::SetArrayRaw(rapidjson::GenericValue*, rapidjson::SizeType, Allocator&) [with Encoding = rapidjson::UTF8<>; Allocator = rapidjson::MemoryPoolAllocator<>; rapidjson::SizeType = unsigned int]': /usr/local/include/rapidjson/document.h:2371:9: required from 'bool rapidjson::GenericDocument::EndArray(rapidjson::SizeType) [with Encoding = rapidjson::UTF8<>; Allocator = rapidjson::MemoryPoolAllocator<>; StackAllocator = rapidjson::CrtAllocator; rapidjson::SizeType = unsigned int]' /usr/local/include/rapidjson/reader.h:1766:18: required from 'rapidjson::GenericReader::IterativeParsingState rapidjson::GenericReader::Transit(rapidjson::GenericReader::IterativeParsingState, rapidjson::GenericReader::Token, rapidjson::GenericReader::IterativeParsingState, InputStream&, Handler&) [with unsigned int parseFlags = 0; InputStream = rapidjson::BasicIStreamWrapper >; Handler = rapidjson::GenericDocument >; SourceEncoding = rapidjson::UTF8<>; TargetEncoding = rapidjson::UTF8<>; StackAllocator = rapidjson::CrtAllocator]' /usr/local/include/rapidjson/reader.h:1832:58: required from 'rapidjson::ParseResult rapidjson::GenericReader::IterativeParse(InputStream&, Handler&) [with unsigned int parseFlags = 0; InputStream = rapidjson::BasicIStreamWrapper >; Handler = rapidjson::GenericDocument >; SourceEncoding = rapidjson::UTF8<>; TargetEncoding = rapidjson::UTF8<>; StackAllocator = rapidjson::CrtAllocator]' /usr/local/include/rapidjson/reader.h:487:46: required from 'rapidjson::ParseResult rapidjson::GenericReader::Parse(InputStream&, Handler&) [with unsigned int parseFlags = 0; InputStream = rapidjson::BasicIStreamWrapper >; Handler = rapidjson::GenericDocument >; SourceEncoding = rapidjson::UTF8<>; TargetEncoding = rapidjson::UTF8<>; StackAllocator = rapidjson::CrtAllocator]' /usr/local/include/rapidjson/document.h:2159:22: required from 'rapidjson::GenericDocument& rapidjson::GenericDocument::ParseStream(InputStream&) [with unsigned int parseFlags = 0; SourceEncoding = rapidjson::UTF8<>; InputStream = rapidjson::BasicIStreamWrapper >; Encoding = rapidjson::UTF8<>; Allocator = rapidjson::MemoryPoolAllocator<>; StackAllocator = rapidjson::CrtAllocator]' /usr/local/include/rapidjson/document.h:2185:70: required from 'rapidjson::GenericDocument& rapidjson::GenericDocument::ParseStream(InputStream&) [with InputStream = rapidjson::BasicIStreamWrapper >; Encoding = rapidjson::UTF8<>; Allocator = rapidjson::MemoryPoolAllocator<>; StackAllocator = rapidjson::CrtAllocator]' /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolInterchange/Parser.cpp:458:22: required from here /usr/local/include/rapidjson/document.h:1939:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'class rapidjson::GenericValue >' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] std::memcpy(e, values, count * sizeof(GenericValue)); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/rapidjson/document.h:540:7: note: 'class rapidjson::GenericValue >' declared here class GenericValue { ^~~~~~~~~~~~ --- Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/all --- --- lib/libRDKitTrajectory.so.1.2018.09.3 --- [ 26%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Trajectory && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so [ 27%] Built target Trajectory --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all --- --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o --- [ 27%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SLNParse/SLNAttribs.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o --- [ 27%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/smarts.tab.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o --- [ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/smiles.tab.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++ -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/rapidjson-1.1.0/include -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolInterchange/Writer.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- smiles.yy: In function 'void yysmiles_error(const char*, std::vector*, RDKit::Atom*&, RDKit::Bond*&, std::__cxx11::list*, void*, int, const char*)': smiles.yy:37:29: warning: unused parameter 'input' [-Wunused-parameter] smiles.yy:39:31: warning: unused parameter 'lastAtom' [-Wunused-parameter] smiles.yy:40:31: warning: unused parameter 'lastBond' [-Wunused-parameter] smiles.yy:41:42: warning: unused parameter 'branchPoints' [-Wunused-parameter] smiles.yy:42:9: warning: unused parameter 'scanner' [-Wunused-parameter] smiles.yy:42:21: warning: unused parameter 'start_token' [-Wunused-parameter] smiles.yy: In function 'void yysmiles_error(const char*, std::vector*, std::__cxx11::list*, void*, int, const char*)': smiles.yy:49:29: warning: unused parameter 'input' [-Wunused-parameter] smiles.yy:51:42: warning: unused parameter 'branchPoints' [-Wunused-parameter] smiles.yy:52:9: warning: unused parameter 'scanner' [-Wunused-parameter] smiles.yy:52:21: warning: unused parameter 'start_token' [-Wunused-parameter] --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o --- smarts.yy: In function 'void yysmarts_error(const char*, std::vector*, RDKit::Atom*&, RDKit::Bond*&, void*, int, const char*)': smarts.yy:24:29: warning: unused parameter 'input' [-Wunused-parameter] smarts.yy:25:46: warning: unused parameter 'ms' [-Wunused-parameter] smarts.yy:26:31: warning: unused parameter 'lastAtom' [-Wunused-parameter] smarts.yy:27:31: warning: unused parameter 'lastBond' [-Wunused-parameter] smarts.yy:28:9: warning: unused parameter 'scanner' [-Wunused-parameter] smarts.yy:28:21: warning: unused parameter 'start_token' [-Wunused-parameter] --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all --- --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o --- [ 28%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SLNParse/sln.tab.cpp --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o --- [ 28%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SLNParse/lex.yysln.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o --- [ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/lex.yysmarts.cpp --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all --- /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp: In function 'void yy_fatal_error(const char*, yyscan_t)': /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp:2585:58: warning: unused parameter 'yyscanner' [-Wunused-parameter] /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp: In function 'void* yysln_alloc(yy_size_t, yyscan_t)': /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp:2917:47: warning: unused parameter 'yyscanner' [-Wunused-parameter] /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp: In function 'void* yysln_realloc(void*, yy_size_t, yyscan_t)': /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp:2922:62: warning: unused parameter 'yyscanner' [-Wunused-parameter] /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp: In function 'void yysln_free(void*, yyscan_t)': /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp:2934:40: warning: unused parameter 'yyscanner' [-Wunused-parameter] --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o --- sln.yy: In function 'void yysln_error(const char*, std::vector*, bool, void*, const char*)': sln.yy:60:43: warning: unused parameter 'ms' [-Wunused-parameter] sln.yy:60:51: warning: unused parameter 'doQ' [-Wunused-parameter] sln.yy:61:13: warning: unused parameter 'scanner' [-Wunused-parameter] --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o --- [ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 28%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/rdqueries.cpp --- Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/all --- --- lib/libRDKitMolInterchange.so.1.2018.09.3 --- [ 28%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MolInterchange && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2018.09.3 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so [ 28%] Built target MolInterchange --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp --- Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all --- --- lib/libRDKitSLNParse.so.1.2018.09.3 --- [ 28%] 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 -std=c++11 -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.1.2018.09.3 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.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2018.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so [ 28%] Built target SLNParse --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 28%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 28%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all --- --- lib/libRDKitSmilesParse.so.1.2018.09.3 --- [ 28%] 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 -std=c++11 -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.1.2018.09.3 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.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so [ 28%] Built target SmilesParse --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 29%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp --- Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/all --- --- Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o --- [ 29%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /construction/science/rdkit/.build/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o --- [ 30%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/Queries.cpp --- Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/all --- --- Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o --- [ 30%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp --- Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/all --- --- rdkit/Chem/rdPartialCharges.so --- [ 31%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 31%] Built target rdPartialCharges --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 31%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /construction/science/rdkit/.build/Code/Numerics/Optimizer && /usr/bin/c++ -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics/Optimizer/BFGSOpt.cpp --- Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/all --- --- lib/libRDKitShapeHelpers.so.1.2018.09.3 --- [ 31%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2018.09.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so [ 31%] Built target ShapeHelpers --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 31%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/Trajectory.cpp --- Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp:12: /usr/local/include/boost/python/extract.hpp: In function 'PyObject* RDKit::computePrincAxesMomentsHelper(bool (*)(const RDKit::Conformer&, Eigen::Matrix3d&, Eigen::Vector3d&, bool, bool, const std::vector*), const RDKit::Conformer&, bool, const boost::python::api::object&)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/all --- --- Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o --- [ 32%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /construction/science/rdkit/.build/Code/Numerics/Optimizer && /usr/bin/c++ -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics/Optimizer/LinearSearch.cpp --- Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/all --- --- rdkit/Chem/rdMolTransforms.so --- [ 32%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 32%] 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 33%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/rapidjson-1.1.0/include -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 34%] Built target rdChemicalFeatures --- Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend --- Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake Scanning dependencies of target graphmolMemTest1 /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build --- Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o --- [ 34%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/memtest1.cpp --- Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/all --- --- lib/libRDKitOptimizer.so.1.2018.09.3 --- [ 34%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/Numerics/Optimizer && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so [ 34%] Built target Optimizer --- Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/depend --- Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/DependInfo.cmake Scanning dependencies of target graphmoltestCanon /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build --- Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/testCanon.cpp.o --- [ 34%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/testCanon.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/graphmoltestCanon.dir/testCanon.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/testCanon.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/Trajectory.cpp:11: /usr/local/include/boost/python/extract.hpp: In function 'RDKit::Snapshot* RDKit::constructSnapshot_wrap(boost::python::list&, double)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp:10: /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = const RDKit::ROMol*]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- rdkit/Chem/rdMolInterchange.so --- [ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so cd /construction/science/rdkit/.build/Code/GraphMol/MolInterchange/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitMolInterchange.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 34%] Built target rdMolInterchange --- Code/GraphMol/CMakeFiles/test-valgrind.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend --- Code/GraphMol/CMakeFiles/test-valgrind.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake Scanning dependencies of target test-valgrind /usr/bin/make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build --- Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o --- [ 34%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/test-valgrind.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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/rdTrajectory.cpp --- Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/all --- --- Code/GraphMol/graphmoltestCanon --- [ 35%] Linking CXX executable graphmoltestCanon cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestCanon.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/graphmoltestCanon.dir/testCanon.cpp.o -o graphmoltestCanon -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 35%] Built target graphmoltestCanon --- Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend --- Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake Scanning dependencies of target graphmolqueryTest /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build --- Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o --- [ 35%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/querytest.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/all --- --- rdkit/Chem/rdqueries.so --- [ 35%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 35%] Built target rdqueries --- Code/GraphMol/CMakeFiles/graphmolIterTest.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend --- Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake Scanning dependencies of target graphmolIterTest /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build --- Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o --- [ 36%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/itertest.cpp --- Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/all --- --- Code/GraphMol/graphmolMemTest1 --- [ 36%] Linking CXX executable graphmolMemTest1 cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 36%] Built target graphmolMemTest1 --- Code/GraphMol/CMakeFiles/graphmolcpTest.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend --- Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake Scanning dependencies of target graphmolcpTest /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build --- Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o --- [ 36%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/cptest.cpp --- Code/GraphMol/CMakeFiles/test-valgrind.dir/all --- --- Code/GraphMol/test-valgrind --- [ 36%] Linking CXX executable test-valgrind cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -o test-valgrind -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 36%] Built target test-valgrind --- Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/all --- /usr/bin/make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend --- Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/SmilesParse /construction/science/rdkit/.build/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake Scanning dependencies of target smiTest2 /usr/bin/make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build --- Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o --- [ 37%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/test2.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/all --- --- rdkit/Chem/rdtrajectory.so --- [ 37%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 37%] Built target rdtrajectory --- Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/all --- /usr/bin/make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend --- Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/SmilesParse /construction/science/rdkit/.build/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake Scanning dependencies of target smaTest1 /usr/bin/make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build --- Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o --- [ 37%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/smatest.cpp --- Code/GraphMol/CMakeFiles/graphmolcpTest.dir/all --- --- Code/GraphMol/graphmolcpTest --- [ 37%] Linking CXX executable graphmolcpTest cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 37%] Built target graphmolcpTest --- 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/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o --- [ 37%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp --- Code/GraphMol/CMakeFiles/graphmolIterTest.dir/all --- --- Code/GraphMol/graphmolIterTest --- [ 37%] Linking CXX executable graphmolIterTest cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 37%] Built target graphmolIterTest --- Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/all --- /usr/bin/make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend --- Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Subgraphs /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Subgraphs /construction/science/rdkit/.build/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake Scanning dependencies of target testSubgraphs1 /usr/bin/make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build --- Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o --- [ 37%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Subgraphs/test1.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/all --- --- Code/GraphMol/SmilesParse/smiTest2 --- [ 37%] Linking CXX executable smiTest2 cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 37%] Built target smiTest2 --- Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/all --- /usr/bin/make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend --- Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Subgraphs /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Subgraphs /construction/science/rdkit/.build/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake Scanning dependencies of target testSubgraphs2 /usr/bin/make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build --- Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o --- [ 38%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Subgraphs/test2.cpp --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:29: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o --- [ 38%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp --- Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/all --- --- Code/GraphMol/graphmolqueryTest --- [ 38%] Linking CXX executable graphmolqueryTest cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 38%] Built target graphmolqueryTest --- 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/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/Subgraphs/CMakeFiles/testSubgraphs1.dir/all --- --- Code/GraphMol/Subgraphs/testSubgraphs1 --- [ 38%] Linking CXX executable testSubgraphs1 cd /construction/science/rdkit/.build/Code/GraphMol/Subgraphs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs1.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 38%] Built target testSubgraphs1 --- 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/FragCatalog/CMakeFiles/FragCatalog.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 Scanning dependencies of target FragCatalog /usr/bin/make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o --- [ 39%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/FragCatalogUtils.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 --- [ 39%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/Filters.cpp --- Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/all --- --- Code/GraphMol/Subgraphs/testSubgraphs2 --- [ 39%] Linking CXX executable testSubgraphs2 cd /construction/science/rdkit/.build/Code/GraphMol/Subgraphs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 39%] Built target testSubgraphs2 --- 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/Fingerprints/CMakeFiles/Fingerprints.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Fingerprints.cpp --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp:26: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/Filters.h:37, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/Filters.cpp:32: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o --- [ 40%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Fingerprints.h:16, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Fingerprints.cpp:15: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp:32: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o --- [ 40%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp --- Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/all --- --- lib/libRDKitChemTransforms.so.1.2018.09.3 --- [ 40%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so [ 40%] Built target ChemTransforms --- Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/all --- /usr/bin/make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend --- Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/PartialCharges /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/PartialCharges /construction/science/rdkit/.build/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake Scanning dependencies of target testPartialCharges /usr/bin/make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build --- Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o --- [ 41%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/PartialCharges && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/PartialCharges/test1.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o --- [ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/PatternFingerprints.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/all --- --- Code/GraphMol/SmilesParse/smaTest1 --- [ 41%] Linking CXX executable smaTest1 cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 41%] Built target smaTest1 --- 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/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp --- Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/all --- --- Code/GraphMol/PartialCharges/testPartialCharges --- [ 42%] Linking CXX executable testPartialCharges cd /construction/science/rdkit/.build/Code/GraphMol/PartialCharges && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 42%] Built target testPartialCharges --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o --- [ 42%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:11: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Fingerprints.h:16, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/PatternFingerprints.cpp:15: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o --- [ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o --- [ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/Filters.h:37, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp:32: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o --- [ 42%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o --- [ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganFingerprints.h:46, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp:37: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp:15: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o --- [ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairs.cpp --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o --- [ 42%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FilterMatchers.cpp --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o --- [ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o --- [ 42%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/FragCatParams.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairs.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairs.cpp:12: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o --- [ 42%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:13: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o --- [ 42%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o --- [ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MACCS.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o --- [ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp:33: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:11: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:11: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp: In instantiation of 'SparseBitVect* RDKit::FingerprintGenerator::getSparseFingerprint(const RDKit::ROMol&, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*) const [with OutputType = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:329:61: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:230:24: warning: comparison of integer expressions of different signedness: 'int' and 'const value_type' {aka 'const unsigned int'} [-Wsign-compare] if (val.second >= dp_fingerprintArguments->d_countBounds[i]) { ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp: In instantiation of 'SparseBitVect* RDKit::FingerprintGenerator::getSparseFingerprint(const RDKit::ROMol&, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*) const [with OutputType = long unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:337:61: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:230:24: warning: comparison of integer expressions of different signedness: 'int' and 'const value_type' {aka 'const unsigned int'} [-Wsign-compare] /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp: In instantiation of 'ExplicitBitVect* RDKit::FingerprintGenerator::getFingerprint(const RDKit::ROMol&, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*) const [with OutputType = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:360:61: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:293:24: warning: comparison of integer expressions of different signedness: 'int' and 'const value_type' {aka 'const unsigned int'} [-Wsign-compare] if (val.second >= dp_fingerprintArguments->d_countBounds[i]) { ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp: In instantiation of 'ExplicitBitVect* RDKit::FingerprintGenerator::getFingerprint(const RDKit::ROMol&, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*) const [with OutputType = long unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:367:61: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:293:24: warning: comparison of integer expressions of different signedness: 'int' and 'const value_type' {aka 'const unsigned int'} [-Wsign-compare] --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/all --- --- lib/libRDKitMolChemicalFeatures.so.1.2018.09.3 --- [ 42%] 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 -std=c++11 -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.1.2018.09.3 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.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2018.09.3 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so [ 42%] Built target MolChemicalFeatures --- 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/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 42%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DReducedGraphs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o --- [ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp --- Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all --- --- lib/libRDKitFilterCatalog.so.1.2018.09.3 --- [ 42%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.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.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so [ 42%] Built target FilterCatalog --- Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/all --- /usr/bin/make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend --- Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SLNParse /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/SLNParse /construction/science/rdkit/.build/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake Scanning dependencies of target testSLNParse /usr/bin/make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build --- Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o --- [ 42%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SLNParse/test.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o --- [ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp --- Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/all --- --- lib/libRDKitFragCatalog.so.1.2018.09.3 --- [ 43%] 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 -std=c++11 -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.1.2018.09.3 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.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2018.09.3 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so [ 43%] Built target FragCatalog --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 43%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:15, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:12: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:15, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:12: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o --- /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp: In instantiation of 'std::vector*> RDKit::AtomPair::AtomPairEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = long unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:133:1: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:138:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:139:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:140:16: warning: unused parameter 'hashResults' [-Wunused-parameter] const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp: In instantiation of 'std::vector*> RDKit::AtomPair::AtomPairEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:133:1: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:138:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:139:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:140:16: warning: unused parameter 'hashResults' [-Wunused-parameter] const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp: In instantiation of 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:83:12: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:86:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp: In instantiation of 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = long unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:83:12: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:86:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o --- /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp: In instantiation of 'RDKit::FingerprintGenerator* RDKit::MorganFingerprint::getMorganGenerator(unsigned int, bool, bool, bool, bool, RDKit::AtomInvariantsGenerator*, RDKit::BondInvariantsGenerator*, uint32_t, std::vector, bool, bool) [with OutputType = unsigned int; uint32_t = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:409:57: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:376:43: warning: unused parameter 'ownsBondInvGen' [-Wunused-parameter] const bool ownsAtomInvGen, const bool ownsBondInvGen) { ~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp: In instantiation of 'RDKit::FingerprintGenerator* RDKit::MorganFingerprint::getMorganGenerator(unsigned int, bool, bool, bool, bool, RDKit::AtomInvariantsGenerator*, RDKit::BondInvariantsGenerator*, uint32_t, std::vector, bool, bool) [with OutputType = long unsigned int; uint32_t = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:418:57: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:376:43: warning: unused parameter 'ownsBondInvGen' [-Wunused-parameter] --- Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/all --- --- lib/libRDKitReducedGraphs.so.1.2018.09.3 --- [ 44%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2018.09.3 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so [ 44%] Built target ReducedGraphs --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 44%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o --- [ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o --- /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp: In instantiation of 'std::vector*> RDKit::MorganFingerprint::MorganEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = long unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:156:1: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:159:39: warning: unused parameter 'ignoreAtoms' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:159:62: warning: unused parameter 'confId' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~^~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:160:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:163:16: warning: unused parameter 'hashResults' [-Wunused-parameter] const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp: In instantiation of 'std::vector*> RDKit::MorganFingerprint::MorganEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:156:1: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:159:39: warning: unused parameter 'ignoreAtoms' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:159:62: warning: unused parameter 'confId' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~^~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:160:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:163:16: warning: unused parameter 'hashResults' [-Wunused-parameter] const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp: In instantiation of 'OutputType RDKit::MorganFingerprint::MorganAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:136:12: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:137:39: warning: unused parameter 'arguments' [-Wunused-parameter] FingerprintArguments *arguments, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:138:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:139:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:140:58: warning: unused parameter 'hashResults' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp: In instantiation of 'OutputType RDKit::MorganFingerprint::MorganAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = long unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:136:12: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:137:39: warning: unused parameter 'arguments' [-Wunused-parameter] FingerprintArguments *arguments, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:138:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:139:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:140:58: warning: unused parameter 'hashResults' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o --- [ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintUtil.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:15, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.h:15, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:11: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 44%] Built target rdSLNParse --- Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/all --- /usr/bin/make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend --- Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics/Optimizer /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/Numerics/Optimizer /construction/science/rdkit/.build/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake Scanning dependencies of target testOptimizer /usr/bin/make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build --- Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o --- [ 44%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd /construction/science/rdkit/.build/Code/Numerics/Optimizer && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics/Optimizer/testOptimizer.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp: In instantiation of 'std::vector*> RDKit::RDKitFP::RDKitFPEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = long unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:111:1: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:114:39: warning: unused parameter 'ignoreAtoms' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:114:62: warning: unused parameter 'confId' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~^~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:115:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:117:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:118:16: warning: unused parameter 'hashResults' [-Wunused-parameter] const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp: In instantiation of 'std::vector*> RDKit::RDKitFP::RDKitFPEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:111:1: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:114:39: warning: unused parameter 'ignoreAtoms' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:114:62: warning: unused parameter 'confId' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~^~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:115:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:117:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:118:16: warning: unused parameter 'hashResults' [-Wunused-parameter] const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp: In instantiation of 'OutputType RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:90:12: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:91:39: warning: unused parameter 'arguments' [-Wunused-parameter] FingerprintArguments *arguments, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:92:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:93:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:94:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:94:58: warning: unused parameter 'hashResults' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp: In instantiation of 'OutputType RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = long unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:90:12: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:91:39: warning: unused parameter 'arguments' [-Wunused-parameter] FingerprintArguments *arguments, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:92:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:93:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:94:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:94:58: warning: unused parameter 'hashResults' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ --- Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:12: /usr/local/include/boost/python/extract.hpp: In function 'boost::python::tuple RDKit::getUnionOfTwoBox(boost::python::tuple, boost::python::tuple)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ In file included from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Conformer.h:14, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ROMol.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:13: /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/point.h:56:31: 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_2018_09_3/Code/Geometry/point.h:56:43: 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_2018_09_3/Code/Geometry/point.h:56:55: 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_2018_09_3/Code/Geometry/point.h:56:31: 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_2018_09_3/Code/Geometry/point.h:56:43: 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_2018_09_3/Code/Geometry/point.h:56:55: 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_2018_09_3/Code/Geometry/point.h:56:31: 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_2018_09_3/Code/Geometry/point.h:56:43: 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_2018_09_3/Code/Geometry/point.h:56:55: 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_2018_09_3/Code/Geometry/point.h:56:31: 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_2018_09_3/Code/Geometry/point.h:56:43: 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_2018_09_3/Code/Geometry/point.h:56:55: 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/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintUtil.h:16, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintUtil.cpp:12: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/all --- --- rdkit/Chem/rdShapeHelpers.so --- [ 44%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 44%] Built target rdShapeHelpers --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o --- [ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- 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 --- [ 44%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/ForceField.cpp --- Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/all --- --- Code/GraphMol/SLNParse/testSLNParse --- [ 44%] Linking CXX executable testSLNParse cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitSLNParse.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 44%] Built target testSLNParse --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/all --- --- Code/Numerics/Optimizer/testOptimizer --- [ 44%] Linking CXX executable testOptimizer cd /construction/science/rdkit/.build/Code/Numerics/Optimizer && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 44%] Built target testOptimizer --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- 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 --- [ 44%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdchem.dir/rdchem.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/rdchem.cpp --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/all --- 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 --- [ 45%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o --- [ 45%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/UFF/AngleBend.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o --- [ 45%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdchem.dir/Table.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/Table.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:15, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:15, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:11: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ In file included from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:11: /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp: In instantiation of 'RDKit::TopologicalTorsion::TopologicalTorsionArguments::TopologicalTorsionArguments(bool, uint32_t, bool, std::vector, uint32_t) [with OutputType = long unsigned int; uint32_t = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:161:7: required from 'RDKit::FingerprintGenerator* RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(bool, uint32_t, RDKit::AtomInvariantsGenerator*, bool, std::vector, uint32_t, bool) [with OutputType = long unsigned int; uint32_t = unsigned int]' /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:183:58: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:26:18: warning: 'RDKit::TopologicalTorsion::TopologicalTorsionArguments::d_torsionAtomCount' will be initialized after [-Wreorder] const uint32_t d_torsionAtomCount; ^~~~~~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:27:76: warning: base 'RDKit::FingerprintArguments' [-Wreorder] FingerprintArguments(countSimulation, countBounds, fpSize){}; ^ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:21:1: warning: when initialized here [-Wreorder] TopologicalTorsionArguments::TopologicalTorsionArguments( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o --- [ 46%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/UFF/BondStretch.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/all --- /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp: In instantiation of 'std::vector*> RDKit::TopologicalTorsion::TopologicalTorsionEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = long unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:58:1: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:61:62: warning: unused parameter 'confId' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~^~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:62:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:64:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp: In instantiation of 'OutputType RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = long unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:43:12: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:44:39: warning: unused parameter 'arguments' [-Wunused-parameter] FingerprintArguments *arguments, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:45:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:46:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:47:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:47:58: warning: unused parameter 'hashResults' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ --- lib/libRDKitFingerprints.so.1.2018.09.3 --- [ 46%] 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 -std=c++11 -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.1.2018.09.3 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/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.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so [ 46%] Built target Fingerprints --- Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/all --- /usr/bin/make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend --- Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ReducedGraphs /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake Scanning dependencies of target testReducedGraphs /usr/bin/make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build --- Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o --- [ 46%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ReducedGraphs/test1.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o --- [ 46%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/UFF/Nonbonded.cpp --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/all --- --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o --- [ 46%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o --- [ 46%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp --- Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/all --- --- Code/GraphMol/ReducedGraphs/testReducedGraphs --- [ 46%] Linking CXX executable testReducedGraphs cd /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitReducedGraphs.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 46%] Built target testReducedGraphs --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 Scanning dependencies of target rdReducedGraphs /usr/bin/make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build --- Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o --- [ 46%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/Wrap.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/rdchem.cpp:12: /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::__cxx11::list; DerivedPolicies = boost::python::detail::final_list_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_list_derived_policies, true>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_list_derived_policies, true> >, long unsigned int>; Data = RDKit::Atom*; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::__cxx11::list; DerivedPolicies = boost::python::detail::final_list_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_list_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_list_derived_policies, false> >, long unsigned int>; Data = RDKit::Atom*; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::__cxx11::list; DerivedPolicies = boost::python::detail::final_list_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_list_derived_policies, true>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_list_derived_policies, true> >, long unsigned int>; Data = RDKit::Bond*; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::__cxx11::list; DerivedPolicies = boost::python::detail::final_list_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_list_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_list_derived_policies, false> >, long unsigned int>; Data = RDKit::Bond*; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o --- [ 46%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/UFF/Inversion.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o --- [ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/Atom.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o --- [ 46%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/UFF/TorsionAngle.cpp --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/all --- --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o --- [ 46%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o --- [ 46%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/UFF/DistanceConstraint.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o --- [ 46%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/UFF/AngleConstraint.cpp --- Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/all --- --- rdkit/Chem/rdReducedGraphs.so --- [ 46%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 47%] Built target rdReducedGraphs --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 47%] 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++ -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o --- [ 47%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/UFF/TorsionConstraint.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o --- [ 48%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/UFF/PositionConstraint.cpp --- Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:12: /usr/local/include/boost/python/extract.hpp: In function 'boost::python::api::object RDKit::GetAtomMatch(boost::python::api::object, int)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- rdkit/Chem/rdMolChemicalFeatures.so --- [ 48%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 48%] Built target rdMolChemicalFeatures --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 48%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o --- [ 48%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/UFF/Params.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o --- [ 48%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF/AngleBend.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/UFF/Params.cpp:19: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:15, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:15: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'const std::vector RDKit::FingerprintWrapper::convertPyArgumentsForBulk(const boost::python::list&)': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:190:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < len; i++) { ~~^~~~~ In file included from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:17: /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/MorganWrapper.cpp: In instantiation of 'RDKit::FingerprintGenerator* RDKit::MorganWrapper::getMorganGenerator(unsigned int, bool, bool, bool, bool, bool, boost::python::api::object&, uint32_t, boost::python::api::object&, boost::python::api::object&) [with OutputType = long unsigned int; uint32_t = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/MorganWrapper.cpp:121:63: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/MorganWrapper.cpp:24:50: warning: unused parameter 'includeRingMembership' [-Wunused-parameter] const bool onlyNonzeroInvariants, const bool includeRingMembership, ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:18: /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/RDKitFPWrapper.cpp: In instantiation of 'RDKit::FingerprintGenerator* RDKit::RDKitFPWrapper::getRDKitFPGenerator(unsigned int, unsigned int, bool, bool, bool, bool, boost::python::api::object&, uint32_t, boost::python::api::object&) [with OutputType = long unsigned int; uint32_t = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/RDKitFPWrapper.cpp:92:63: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/RDKitFPWrapper.cpp:27:28: warning: unused variable 'bondInvariantsGenerator' [-Wunused-variable] BondInvariantsGenerator *bondInvariantsGenerator = nullptr; ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:19: /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/TopologicalTorsionWrapper.cpp: In instantiation of 'RDKit::FingerprintGenerator* RDKit::TopologicalTorsionWrapper::getTopologicalTorsionFPGenerator(bool, uint32_t, bool, boost::python::api::object&, uint32_t, boost::python::api::object&) [with OutputType = long unsigned int; uint32_t = unsigned int]': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/TopologicalTorsionWrapper.cpp:75:63: required from here /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/TopologicalTorsionWrapper.cpp:26:28: warning: unused variable 'bondInvariantsGenerator' [-Wunused-variable] BondInvariantsGenerator *bondInvariantsGenerator = nullptr; ^~~~~~~~~~~~~~~~~~~~~~~ --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o --- [ 48%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF/BondStretch.cpp --- Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Fingerprints.h:16, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/SubstructLibrary.h:39, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp:31: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o --- [ 48%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF/StretchBend.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o --- [ 48%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/Bond.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o --- [ 48%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF/OopBend.cpp --- Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/all --- --- lib/libRDKitSubstructLibrary.so.1.2018.09.3 --- [ 49%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2018.09.3 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so [ 49%] Built target SubstructLibrary --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o --- [ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/Mol.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o --- [ 50%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF/TorsionAngle.cpp --- Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:13: /usr/local/include/boost/python/extract.hpp: In function 'void RDKit::FingerprintWrapper::convertPyArguments(boost::python::api::object, boost::python::api::object, boost::python::api::object, boost::python::api::object, std::vector*&, std::vector*&, std::vector*&, std::vector*&)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'const std::vector RDKit::FingerprintWrapper::convertPyArgumentsForBulk(const boost::python::list&)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- rdkit/Chem/rdFingerprintGenerator.so --- [ 51%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 51%] Built target rdFingerprintGenerator --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o --- [ 51%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/Conformer.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o --- [ 51%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF/Nonbonded.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o --- [ 52%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF/DistanceConstraint.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o --- [ 52%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF/AngleConstraint.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o --- [ 52%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF/TorsionConstraint.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o --- [ 52%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF/PositionConstraint.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/Conformer.cpp:13: /usr/local/include/boost/python/extract.hpp: In function 'void RDKit::SetAtomPos(RDKit::Conformer*, unsigned int, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o --- [ 52%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/RingInfo.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o --- [ 52%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd /construction/science/rdkit/.build/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF/Params.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o --- [ 52%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/EditableMol.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF/Params.cpp:21: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o --- [ 52%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/MonomerInfo.cpp --- Code/ForceField/CMakeFiles/ForceField.dir/all --- --- lib/libRDKitForceField.so.1.2018.09.3 --- [ 52%] 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 -std=c++11 -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.1.2018.09.3 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.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/ForceField && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so [ 52%] 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o --- [ 53%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/RingInfo.cpp:12: /usr/local/include/boost/python/extract.hpp: In function 'void {anonymous}::addRing(RDKit::RingInfo*, boost::python::api::object, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o --- [ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o --- [ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/MolBundle.cpp --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/all --- --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o --- [ 53%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o --- [ 53%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o --- [ 53%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o --- [ 53%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o --- [ 53%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all --- --- rdkit/Chem/rdchem.so --- [ 54%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 54%] Built target rdchem --- Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp:22: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- lib/libRDKitForceFieldHelpers.so.1.2018.09.3 --- [ 54%] 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 -std=c++11 -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.1.2018.09.3 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.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so [ 54%] Built target ForceFieldHelpers --- Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/all --- --- Code/DistGeom/CMakeFiles/DistGeometry.dir/all --- --- Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/all --- --- Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/all --- --- 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/DistGeom/CMakeFiles/DistGeometry.dir/all --- /usr/bin/make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend --- 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/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/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/all --- --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/all --- --- Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend --- --- Code/DistGeom/CMakeFiles/DistGeometry.dir/all --- --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/all --- --- Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend --- --- Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- Code/DistGeom/CMakeFiles/DistGeometry.dir/all --- Scanning dependencies of target DistGeometry --- Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/all --- Scanning dependencies of target rdForceFieldHelpers --- Code/DistGeom/CMakeFiles/DistGeometry.dir/all --- /usr/bin/make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build --- 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/build --- Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o --- --- Code/DistGeom/CMakeFiles/DistGeometry.dir/all --- --- Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o --- --- Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o --- --- Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/all --- [ 54%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp --- Code/DistGeom/CMakeFiles/DistGeometry.dir/all --- [ 54%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o cd /construction/science/rdkit/.build/Code/DistGeom && /usr/bin/c++ -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DistGeom/TriangleSmooth.cpp --- Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o --- [ 54%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o cd /construction/science/rdkit/.build/Code/DistGeom && /usr/bin/c++ -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DistGeom/DistGeomUtils.cpp --- Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/all --- 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 --- [ 54%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /construction/science/rdkit/.build/Code/ForceField/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/Wrap/ForceField.cpp --- Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/all --- 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 --- [ 54%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/bin/c++ -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolAlign/AlignMolecules.cpp --- Code/DistGeom/CMakeFiles/DistGeometry.dir/all --- --- Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o --- [ 55%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o cd /construction/science/rdkit/.build/Code/DistGeom && /usr/bin/c++ -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DistGeom/DistViolationContrib.cpp --- Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o --- [ 55%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o cd /construction/science/rdkit/.build/Code/DistGeom && /usr/bin/c++ -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DistGeom/ChiralViolationContrib.cpp --- Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/all --- --- Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/O3AAlignMolecules.cpp.o --- [ 56%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/O3AAlignMolecules.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/bin/c++ -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolAlign.dir/O3AAlignMolecules.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp --- Code/DistGeom/CMakeFiles/DistGeometry.dir/all --- --- lib/libRDKitDistGeometry.so.1.2018.09.3 --- [ 56%] 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 -std=c++11 -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.1.2018.09.3 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.1.2018.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/DistGeom && /usr/local/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2018.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so [ 56%] Built target DistGeometry --- Code/DistGeom/CMakeFiles/testDistGeom.dir/all --- --- Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/all --- --- Code/DistGeom/CMakeFiles/testDistGeom.dir/all --- /usr/bin/make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend --- 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/CMakeFiles/testDistGeom.dir/all --- --- Code/DistGeom/CMakeFiles/testDistGeom.dir/depend --- --- Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/all --- --- Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend --- --- Code/DistGeom/CMakeFiles/testDistGeom.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DistGeom /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/DistGeom /construction/science/rdkit/.build/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --- Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- Code/DistGeom/CMakeFiles/testDistGeom.dir/all --- Scanning dependencies of target testDistGeom /usr/bin/make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build --- Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o --- [ 56%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o cd /construction/science/rdkit/.build/Code/DistGeom && /usr/bin/c++ -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DistGeom/testDistGeom.cpp --- Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/all --- 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 --- [ 56%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /construction/science/rdkit/.build/Code/DistGeom/Wrap && /usr/bin/c++ -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DistGeom/Wrap/DistGeom.cpp --- Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/Wrap/ForceField.cpp:12: /usr/local/include/boost/python/extract.hpp: In member function 'double ForceFields::PyForceField::calcEnergyWithPos(const boost::python::api::object&)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In member function 'PyObject* ForceFields::PyForceField::calcGradWithPos(const boost::python::api::object&)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/all --- --- rdkit/Chem/rdForceFieldHelpers.so --- [ 56%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 57%] Built target rdForceFieldHelpers --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 57%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp --- Code/DistGeom/CMakeFiles/testDistGeom.dir/all --- --- Code/DistGeom/testDistGeom --- [ 57%] Linking CXX executable testDistGeom cd /construction/science/rdkit/.build/Code/DistGeom && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitDistGeometry.so.1.2018.09.3 ../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 57%] Built target testDistGeom --- Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/all --- --- Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o --- [ 57%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/DistGeomHelpers/Embedder.cpp --- Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/all --- --- rdkit/ForceField/rdForceField.so --- [ 57%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 57%] Built target rdForceField --- Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/all --- --- lib/libRDKitMolAlign.so.1.2018.09.3 --- [ 57%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o CMakeFiles/MolAlign.dir/O3AAlignMolecules.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so [ 57%] Built target MolAlign --- External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/all --- --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 Scanning dependencies of target rdCoordGen /usr/bin/make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build --- External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o --- [ 57%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o cd /construction/science/rdkit/.build/External/CoordGen/Wrap && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCoordGen_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/Wrap/rdCoordGen.cpp --- 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 --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o --- [ 57%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Depictor && /usr/bin/c++ -DDepictor_EXPORTS -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Depictor/RDDepictor.cpp --- Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/all --- --- rdkit/DistanceGeometry/DistGeom.so --- [ 58%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 58%] Built target DistGeom --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/all --- --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o --- [ 58%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Depictor && /usr/bin/c++ -DDepictor_EXPORTS -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Depictor/EmbeddedFrag.cpp --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o --- [ 58%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Depictor && /usr/bin/c++ -DDepictor_EXPORTS -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Depictor/DepictUtils.cpp --- Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/all --- --- lib/libRDKitDistGeomHelpers.so.1.2018.09.3 --- [ 58%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDistGeometry.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so [ 58%] Built target DistGeomHelpers --- External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/Wrap/rdCoordGen.cpp:12: /usr/local/include/boost/python/extract.hpp: In function 'void RDKit::{anonymous}::SetCoordMap(RDKit::CoordGen::CoordGenParams*, boost::python::dict&)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- rdkit/Chem/rdCoordGen.so --- [ 58%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 58%] Built target rdCoordGen --- Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/all --- --- lib/libRDKitDepictor.so.1.2018.09.3 --- [ 58%] 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 -std=c++11 -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.1.2018.09.3 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 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Depictor && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so [ 58%] Built target Depictor --- 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/FileParsers/CMakeFiles/FileParsers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 Scanning dependencies of target FileParsers /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o --- --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o --- [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/MolFileWriter.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o --- [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o --- [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/MolFileStereochem.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o --- [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/Mol2FileParser.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o --- [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/MolFileParser.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/Mol2FileParser.cpp:40: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp:12: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/MolFileParser.cpp:24: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o --- [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/SDMolSupplier.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o --- [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/SDWriter.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o --- [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/SDMolSupplier.cpp:13: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp:13: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o --- [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/SmilesWriter.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o --- [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/TDTMolSupplier.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o --- [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/TDTWriter.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o --- [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/TplFileParser.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o --- [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/TplFileWriter.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o --- [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/PDBParser.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/TplFileParser.cpp:20: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o --- [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/PDBWriter.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o --- [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/PDBSupplier.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o --- [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/MaeMolSupplier.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o --- [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/ProximityBonds.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o --- [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/SequenceParsers.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o --- [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/SequenceWriters.cpp --- Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o --- [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/SVGParser.cpp --- lib/libRDKitFileParsers.so.1.2018.09.3 --- [ 61%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.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/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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so [ 62%] Built target FileParsers --- External/CoordGen/CMakeFiles/testCoordGen.dir/all --- --- Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/all --- --- Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/all --- --- Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/all --- --- Code/GraphMol/CMakeFiles/graphmolTest1.dir/all --- --- External/CoordGen/CMakeFiles/testCoordGen.dir/all --- /usr/bin/make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend --- Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/all --- /usr/bin/make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend --- Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/all --- /usr/bin/make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend --- Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend --- Code/GraphMol/CMakeFiles/graphmolTest1.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend --- External/CoordGen/CMakeFiles/testCoordGen.dir/all --- --- External/CoordGen/CMakeFiles/testCoordGen.dir/depend --- --- Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/all --- --- Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend --- --- Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/all --- --- Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend --- --- External/CoordGen/CMakeFiles/testCoordGen.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen /construction/science/rdkit/.build /construction/science/rdkit/.build/External/CoordGen /construction/science/rdkit/.build/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake --- Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/all --- --- Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend --- --- Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/ForceField/MMFF /construction/science/rdkit/.build/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --- Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --- Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/UFF /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/ForceField/UFF /construction/science/rdkit/.build/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --- Code/GraphMol/CMakeFiles/graphmolTest1.dir/all --- --- Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --- Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/all --- Scanning dependencies of target testMMFFForceField /usr/bin/make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build --- Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/all --- Scanning dependencies of target graphmolMolOpsTest /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build --- Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/all --- --- Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o --- [ 62%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o cd /construction/science/rdkit/.build/Code/ForceField/MMFF && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/MMFF/testMMFFForceField.cpp --- Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/all --- --- Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o --- --- Code/GraphMol/CMakeFiles/graphmolTest1.dir/all --- Scanning dependencies of target graphmolTest1 /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build --- Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/all --- [ 62%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/molopstest.cpp --- External/CoordGen/CMakeFiles/testCoordGen.dir/all --- Scanning dependencies of target testCoordGen /usr/bin/make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build --- Code/GraphMol/CMakeFiles/graphmolTest1.dir/all --- --- Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o --- --- Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/all --- Scanning dependencies of target testUFFForceField /usr/bin/make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build --- Code/GraphMol/CMakeFiles/graphmolTest1.dir/all --- [ 62%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/test1.cpp --- External/CoordGen/CMakeFiles/testCoordGen.dir/all --- --- External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o --- --- Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/all --- --- Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o --- --- External/CoordGen/CMakeFiles/testCoordGen.dir/all --- [ 62%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/bin/c++ -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/External/CoordGen/test.cpp --- Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/all --- [ 63%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o cd /construction/science/rdkit/.build/Code/ForceField/UFF && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ForceField/UFF/testUFFForceField.cpp --- External/CoordGen/CMakeFiles/testCoordGen.dir/all --- --- External/CoordGen/testCoordGen --- [ 63%] Linking CXX executable testCoordGen cd /construction/science/rdkit/.build/External/CoordGen && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../lib/libRDKitDepictor.so.1.2018.09.3 ../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../lib/libRDKitAlignment.so.1.2018.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 63%] Built target testCoordGen --- Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend --- Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake Scanning dependencies of target graphmoltestChirality /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build --- Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o --- [ 63%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/testChirality.cpp --- Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/all --- --- Code/ForceField/UFF/testUFFForceField --- [ 63%] Linking CXX executable testUFFForceField cd /construction/science/rdkit/.build/Code/ForceField/UFF && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 63%] Built target testUFFForceField --- Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend --- Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake Scanning dependencies of target graphmoltestPickler /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build --- Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o --- [ 63%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/testPickler.cpp --- Code/GraphMol/CMakeFiles/graphmolTest1.dir/all --- --- Code/GraphMol/graphmolTest1 --- [ 63%] Linking CXX executable graphmolTest1 cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../lib/libRDKitDepictor.so.1.2018.09.3 ../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../lib/libRDKitAlignment.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 63%] Built target graphmolTest1 --- Code/GraphMol/CMakeFiles/molBundleTest.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend --- Code/GraphMol/CMakeFiles/molBundleTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake Scanning dependencies of target molBundleTest /usr/bin/make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build --- Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o --- [ 63%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/testMolBundle.cpp --- Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/all --- --- Code/ForceField/MMFF/testMMFFForceField --- [ 63%] Linking CXX executable testMMFFForceField cd /construction/science/rdkit/.build/Code/ForceField/MMFF && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.3 ../../../lib/libRDKitDistGeometry.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 63%] Built target testMMFFForceField --- Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend --- Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake Scanning dependencies of target resMolSupplierTest /usr/bin/make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build --- Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o --- [ 63%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/resMolSupplierTest.cpp --- Code/GraphMol/CMakeFiles/molBundleTest.dir/all --- --- Code/GraphMol/molBundleTest --- [ 63%] Linking CXX executable molBundleTest cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../lib/libRDKitDepictor.so.1.2018.09.3 ../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../lib/libRDKitAlignment.so.1.2018.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 63%] Built target molBundleTest --- Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend --- Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake Scanning dependencies of target graphmoltestPicklerGlobalSetting /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build --- Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o --- [ 63%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/testPicklerGlobalSettings.cpp --- Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/all --- --- Code/GraphMol/resMolSupplierTest --- [ 64%] Linking CXX executable resMolSupplierTest cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../lib/libRDKitDepictor.so.1.2018.09.3 ../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../lib/libRDKitAlignment.so.1.2018.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 64%] Built target resMolSupplierTest --- Code/GraphMol/CMakeFiles/hanoiTest.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend --- Code/GraphMol/CMakeFiles/hanoiTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake Scanning dependencies of target hanoiTest /usr/bin/make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build --- Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o --- [ 64%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/hanoitest.cpp --- Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/all --- --- Code/GraphMol/graphmoltestPicklerGlobalSetting --- [ 64%] Linking CXX executable graphmoltestPicklerGlobalSetting cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../lib/libRDKitDepictor.so.1.2018.09.3 ../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../lib/libRDKitAlignment.so.1.2018.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 64%] Built target graphmoltestPicklerGlobalSetting --- Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/all --- /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend --- Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol /construction/science/rdkit/.build/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake Scanning dependencies of target graphmolTestsCatch /usr/bin/make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build --- Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/all --- --- Code/GraphMol/graphmoltestPickler --- --- Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/all --- --- Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_tests.cpp.o --- --- Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/all --- [ 64%] Linking CXX executable graphmoltestPickler cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 --- Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/all --- [ 65%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_tests.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/graphmolTestsCatch.dir/catch_tests.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/catch_tests.cpp --- Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/all --- /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../lib/libRDKitDepictor.so.1.2018.09.3 ../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../lib/libRDKitAlignment.so.1.2018.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 65%] Built target graphmoltestPickler --- Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/all --- /usr/bin/make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend --- Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Depictor /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Depictor /construction/science/rdkit/.build/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake Scanning dependencies of target testDepictor /usr/bin/make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build --- Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o --- [ 65%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Depictor && /usr/bin/c++ -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Depictor/testDepictor.cpp --- Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/all --- --- Code/GraphMol/graphmoltestChirality --- [ 65%] Linking CXX executable graphmoltestChirality cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../lib/libRDKitDepictor.so.1.2018.09.3 ../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../lib/libRDKitAlignment.so.1.2018.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 65%] Built target graphmoltestChirality --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 65%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp --- Code/GraphMol/CMakeFiles/hanoiTest.dir/all --- --- Code/GraphMol/hanoiTest --- [ 66%] Linking CXX executable hanoiTest cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../lib/libRDKitDepictor.so.1.2018.09.3 ../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../lib/libRDKitAlignment.so.1.2018.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 66%] Built target hanoiTest --- Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/all --- /usr/bin/make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend --- Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/SmilesParse /construction/science/rdkit/.build/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake Scanning dependencies of target smiTest1 /usr/bin/make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build --- Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o --- [ 66%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/smiTest1.dir/test.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/test.cpp --- Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/all --- --- Code/GraphMol/Depictor/testDepictor --- [ 66%] Linking CXX executable testDepictor cd /construction/science/rdkit/.build/Code/GraphMol/Depictor && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 66%] Built target testDepictor --- Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/all --- /usr/bin/make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend --- Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/SmilesParse /construction/science/rdkit/.build/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake Scanning dependencies of target cxsmilesTest /usr/bin/make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build --- Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o --- [ 66%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/cxsmiles_test.cpp --- Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp:11: /usr/local/include/boost/python/extract.hpp: In function 'unsigned int RDDepict::Compute2DCoords(RDKit::ROMol&, bool, bool, boost::python::dict&, unsigned int, unsigned int, int, bool, double, bool)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- rdkit/Chem/rdDepictor.so --- [ 66%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 67%] Built target rdDepictor --- Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/all --- /usr/bin/make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend --- Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/SmilesParse /construction/science/rdkit/.build/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake --- Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/all --- --- Code/GraphMol/SmilesParse/cxsmilesTest --- [ 68%] Linking CXX executable cxsmilesTest cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 68%] Built target cxsmilesTest --- Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/all --- /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend --- Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FileParsers /construction/science/rdkit/.build/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --- Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/all --- Scanning dependencies of target smiTestCatch /usr/bin/make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build --- Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o --- [ 68%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SmilesParse/catch_tests.cpp --- Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/all --- Scanning dependencies of target testMol2ToMol /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build --- Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o --- [ 68%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/testMol2ToMol.cpp --- Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/all --- --- Code/GraphMol/graphmolMolOpsTest --- [ 68%] Linking CXX executable graphmolMolOpsTest cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../lib/libRDKitDepictor.so.1.2018.09.3 ../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../lib/libRDKitAlignment.so.1.2018.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 68%] Built target graphmolMolOpsTest --- Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/all --- /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend --- Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FileParsers /construction/science/rdkit/.build/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake Scanning dependencies of target testExtendedStereoParsing /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build --- Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o --- [ 68%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp --- Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/all --- --- Code/GraphMol/FileParsers/testMol2ToMol --- [ 68%] Linking CXX executable testMol2ToMol cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 68%] Built target testMol2ToMol --- Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/all --- /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend --- Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FileParsers /construction/science/rdkit/.build/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake Scanning dependencies of target testMolWriter /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build --- Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o --- [ 68%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/testMolWriter.cpp --- Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/all --- --- Code/GraphMol/FileParsers/testExtendedStereoParsing --- [ 68%] Linking CXX executable testExtendedStereoParsing cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 68%] Built target testExtendedStereoParsing --- Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/all --- /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend --- Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FileParsers /construction/science/rdkit/.build/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake Scanning dependencies of target testMolSupplier /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build --- Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o --- --- Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/testMolWriter.cpp:21: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/all --- [ 68%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/testMolSupplier.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/all --- --- Code/GraphMol/SmilesParse/smiTest1 --- [ 68%] Linking CXX executable smiTest1 cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 68%] Built target smiTest1 --- Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/all --- /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend --- Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FileParsers /construction/science/rdkit/.build/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake Scanning dependencies of target fileParsersCatchTest /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build --- Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/catch_tests.cpp.o --- [ 68%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/catch_tests.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/fileParsersCatchTest.dir/catch_tests.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/catch_tests.cpp --- Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/all --- --- Code/GraphMol/FileParsers/testMolWriter --- [ 69%] Linking CXX executable testMolWriter cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 69%] Built target testMolWriter --- Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/all --- /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend --- Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FileParsers /construction/science/rdkit/.build/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake Scanning dependencies of target fileParsersTest1 /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build --- Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o --- [ 69%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/test1.cpp --- Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/all --- --- Code/GraphMol/FileParsers/testMolSupplier --- [ 69%] Linking CXX executable testMolSupplier cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 69%] Built target testMolSupplier --- Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/all --- /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend --- Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FileParsers /construction/science/rdkit/.build/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake Scanning dependencies of target testTplParser /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build --- Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o --- [ 69%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/testTpls.cpp --- Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/all --- --- Code/GraphMol/graphmolTestsCatch --- [ 69%] Linking CXX executable graphmolTestsCatch cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/graphmolTestsCatch.dir/catch_tests.cpp.o -o graphmolTestsCatch -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../lib/libRDKitDepictor.so.1.2018.09.3 ../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../lib/libRDKitAlignment.so.1.2018.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 69%] Built target graphmolTestsCatch --- Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/all --- /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend --- Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FileParsers /construction/science/rdkit/.build/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake Scanning dependencies of target testSequence /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build --- Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o --- [ 69%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FileParsers/testSequence.cpp --- Code/GraphMol/FileParsers/testSequence --- [ 69%] Linking CXX executable testSequence cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 69%] Built target testSequence --- Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/all --- /usr/bin/make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend --- Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Substruct /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Substruct /construction/science/rdkit/.build/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake Scanning dependencies of target testSubstructMatch /usr/bin/make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build --- Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o --- [ 69%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Substruct && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Substruct/test1.cpp --- Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/all --- --- Code/GraphMol/FileParsers/testTplParser --- [ 69%] Linking CXX executable testTplParser cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 69%] Built target testTplParser --- Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/all --- /usr/bin/make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend --- Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemTransforms /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake Scanning dependencies of target testChemTransforms /usr/bin/make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build --- Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o --- [ 69%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemTransforms/testChemTransforms.cpp --- Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/all --- --- Code/GraphMol/SmilesParse/smiTestCatch --- [ 69%] Linking CXX executable smiTestCatch cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 69%] Built target smiTestCatch --- Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/all --- /usr/bin/make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend --- Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake Scanning dependencies of target filterCatalogTest /usr/bin/make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build --- Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o --- [ 69%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp:35: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/all --- --- Code/GraphMol/Substruct/testSubstructMatch --- [ 69%] Linking CXX executable testSubstructMatch cd /construction/science/rdkit/.build/Code/GraphMol/Substruct && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 69%] Built target testSubstructMatch --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 69%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp --- Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/all --- --- Code/GraphMol/FilterCatalog/filterCatalogTest --- [ 69%] Linking CXX executable filterCatalogTest cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 69%] Built target filterCatalogTest --- Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/all --- /usr/bin/make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend --- Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FragCatalog /construction/science/rdkit/.build/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake Scanning dependencies of target testFragCatalog /usr/bin/make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build --- Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o --- [ 69%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/test1.cpp --- Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/all --- --- Code/GraphMol/FileParsers/fileParsersCatchTest --- [ 69%] Linking CXX executable fileParsersCatchTest cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/fileParsersCatchTest.dir/catch_tests.cpp.o -o fileParsersCatchTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 69%] Built target fileParsersCatchTest --- 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/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o --- --- Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/all --- --- Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o --- [ 69%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp --- Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/all --- --- Code/GraphMol/ChemTransforms/testChemTransforms --- --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- [ 69%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o --- Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/all --- [ 69%] Linking CXX executable testChemTransforms cd /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp --- Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/all --- [ 69%] Built target testChemTransforms --- 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/Descriptors/CMakeFiles/Descriptors.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 70%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/Crippen.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/Crippen.cpp --- Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/FragCatGenerator.h:14, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/test1.cpp:18: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/Crippen.cpp:20: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o --- [ 70%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp --- Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/all --- --- Code/GraphMol/FragCatalog/testFragCatalog --- [ 71%] Linking CXX executable testFragCatalog cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFragCatalog.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 71%] Built target testFragCatalog --- Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/all --- /usr/bin/make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend --- Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Fingerprints /construction/science/rdkit/.build/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake Scanning dependencies of target testFingerprints /usr/bin/make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build --- Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o --- [ 71%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/test1.cpp --- Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/all --- --- Code/GraphMol/FileParsers/fileParsersTest1 --- [ 71%] Linking CXX executable fileParsersTest1 cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 71%] Built target fileParsersTest1 --- Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/all --- /usr/bin/make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend --- Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Fingerprints /construction/science/rdkit/.build/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --- Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:35: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/all --- Scanning dependencies of target testFingerprintGenerators /usr/bin/make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build --- Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o --- [ 71%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o --- [ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/MolDescriptors.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Fingerprints.h:16, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/test1.cpp:18: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/FragCatGenerator.h:14, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp:15: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairs.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:14: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ In file included from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RDKitBase.h:21, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:12: /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp: In function 'void testAtomPairNonSparseBitvector()': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:225:42: warning: comparison of integer expressions of different signedness: 'int' and '__gnu_cxx::__alloc_traits, unsigned int>::value_type' {aka 'unsigned int'} [-Wsign-compare] TEST_ASSERT(isSet == (it->second >= defaultCountBounds[i])); /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/Invariant.h:152:9: note: in definition of macro 'TEST_ASSERT' if (!(expr)) { \ ^~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:242:42: warning: comparison of integer expressions of different signedness: 'int' and '__gnu_cxx::__alloc_traits, unsigned int>::value_type' {aka 'unsigned int'} [-Wsign-compare] TEST_ASSERT(isSet == (it->second >= defaultCountBounds[i])); /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/Invariant.h:152:9: note: in definition of macro 'TEST_ASSERT' if (!(expr)) { \ ^~~~ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp: In function 'void testBulkFP()': /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:2388:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector*>::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < results->size(); i++) { ~~^~~~~~~~~~~~~~~~~ --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o --- [ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/MolSurf.cpp --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o --- [ 72%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o --- [ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/Lipinski.cpp --- Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector >; DerivedPolicies = boost::python::detail::final_vector_derived_policies >, false>; ProxyHandler = boost::python::detail::proxy_helper >, boost::python::detail::final_vector_derived_policies >, false>, boost::python::detail::container_element >, long unsigned int, boost::python::detail::final_vector_derived_policies >, false> >, long unsigned int>; Data = std::pair; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::FilterMatch; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, true> >, long unsigned int>; Data = RDKit::ROMol*; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector >; DerivedPolicies = boost::python::detail::final_vector_derived_policies >, true>; ProxyHandler = boost::python::detail::no_proxy_helper >, boost::python::detail::final_vector_derived_policies >, true>, boost::python::detail::container_element >, long unsigned int, boost::python::detail::final_vector_derived_policies >, true> >, long unsigned int>; Data = boost::shared_ptr; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/all --- --- Code/GraphMol/Fingerprints/testFingerprintGenerators --- [ 72%] Linking CXX executable testFingerprintGenerators cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 72%] Built target testFingerprintGenerators --- Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/all --- /usr/bin/make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend --- Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolTransforms /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolTransforms /construction/science/rdkit/.build/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake Scanning dependencies of target testMolTransforms /usr/bin/make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build --- Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o --- [ 72%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolTransforms && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolTransforms/test1.cpp --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/FragCatGenerator.h:14, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp:17: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/all --- --- rdkit/Chem/rdfiltercatalog.so --- [ 72%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o --- [ 72%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp --- Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/all --- [ 72%] Built target rdfiltercatalog --- Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/all --- /usr/bin/make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend --- Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/MMFF /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/MMFF /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake Scanning dependencies of target testMMFFForceFieldHelpers /usr/bin/make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build --- Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o --- [ 73%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o --- [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp --- Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/all --- --- Code/GraphMol/Fingerprints/testFingerprints --- [ 73%] Linking CXX executable testFingerprints cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 73%] Built target testFingerprints --- Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/all --- /usr/bin/make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend --- Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/UFF /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/UFF /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake Scanning dependencies of target testUFFForceFieldHelpers /usr/bin/make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build --- Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o --- [ 73%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp --- Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/all --- --- Code/GraphMol/MolTransforms/testMolTransforms --- [ 73%] Linking CXX executable testMolTransforms cd /construction/science/rdkit/.build/Code/GraphMol/MolTransforms && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 73%] Built target testMolTransforms --- Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/all --- /usr/bin/make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend --- Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/CrystalFF /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/CrystalFF /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake Scanning dependencies of target testCrystalForceField /usr/bin/make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build --- Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o --- [ 73%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/FragCatGenerator.h:14, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp:14: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o --- [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/MQN.cpp --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o --- [ 73%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o --- [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/Property.cpp --- Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/all --- --- Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers --- [ 73%] Linking CXX executable testMMFFForceFieldHelpers cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 73%] Built target testMMFFForceFieldHelpers --- Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/all --- /usr/bin/make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend --- Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/DistGeomHelpers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake Scanning dependencies of target testDistGeomHelpers /usr/bin/make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build --- Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o --- [ 73%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp --- Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/all --- --- Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField --- [ 74%] Linking CXX executable testCrystalForceField cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 74%] Built target testCrystalForceField --- 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/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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 74%] 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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/FragFPGenerator.h:15, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp:14: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/all --- --- Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers --- [ 74%] Linking CXX executable testUFFForceFieldHelpers cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/UFF && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 74%] Built target testUFFForceFieldHelpers --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/all --- /usr/bin/make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolChemicalFeatures /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake Scanning dependencies of target testFeatures /usr/bin/make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o --- [ 74%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp --- Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/all --- --- rdkit/Chem/rdfragcatalog.so --- [ 74%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 74%] Built target rdfragcatalog --- Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/all --- /usr/bin/make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend --- Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ShapeHelpers /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o --- [ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/AUTOCORR2D.cpp --- Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/all --- Scanning dependencies of target testShapeHelpers /usr/bin/make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build --- Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o --- [ 75%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:17: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o --- [ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o --- [ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp --- Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/all --- --- Code/GraphMol/ShapeHelpers/testShapeHelpers --- [ 76%] Linking CXX executable testShapeHelpers cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitShapeHelpers.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 76%] Built target testShapeHelpers --- Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/all --- /usr/bin/make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend --- Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolCatalog /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolCatalog /construction/science/rdkit/.build/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake Scanning dependencies of target testMolCatalog /usr/bin/make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build --- Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o --- [ 76%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolCatalog && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolCatalog/test1.cpp --- Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/all --- --- Code/GraphMol/DistGeomHelpers/testDistGeomHelpers --- [ 76%] Linking CXX executable testDistGeomHelpers cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.3 ../../../lib/libRDKitDistGeometry.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 76%] Built target testDistGeomHelpers --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 76%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp --- Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/all --- --- Code/GraphMol/MolChemicalFeatures/testFeatures --- [ 76%] Linking CXX executable testFeatures cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitMolChemicalFeatures.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 76%] Built target testFeatures --- 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/FMCS/CMakeFiles/FMCS.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o --- [ 77%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/bin/c++ -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/FMCS.cpp --- Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: /usr/local/include/boost/python/extract.hpp: In function 'RDKit::INT_VECT RDKit::EmbedMultipleConfs(RDKit::ROMol&, unsigned int, unsigned int, int, bool, bool, double, bool, unsigned int, double, boost::python::dict&, double, bool, bool, int, bool, bool, bool)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'int RDKit::EmbedMolecule(RDKit::ROMol&, unsigned int, int, bool, bool, double, bool, unsigned int, boost::python::dict&, double, bool, bool, bool, bool, bool)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolCatalog/MolCatalog.h:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolCatalog/test1.cpp:12: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o --- --- Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/all --- --- rdkit/Chem/rdDistGeom.so --- [ 77%] 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 --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- [ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/USRDescriptor.cpp --- Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/all --- /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 77%] Built target rdDistGeom --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 77%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MMPA && /usr/bin/c++ -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MMPA/MMPA.cpp --- Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolCatalog/MolCatalog.h:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp:8: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/all --- --- Code/GraphMol/MolCatalog/testMolCatalog --- [ 78%] Linking CXX executable testMolCatalog cd /construction/science/rdkit/.build/Code/GraphMol/MolCatalog && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitMolCatalog.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 78%] Built target testMolCatalog --- Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/all --- /usr/bin/make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend --- Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Trajectory /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Trajectory /construction/science/rdkit/.build/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake Scanning dependencies of target trajectoryTest /usr/bin/make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build --- Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o --- [ 78%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Trajectory && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Trajectory/trajectoryTest.cpp --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/all --- --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o --- [ 78%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/bin/c++ -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/Seed.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o --- [ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/EEM.cpp --- Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/all --- --- rdkit/Chem/rdMolCatalog.so --- [ 78%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 78%] Built target rdMolCatalog --- Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/all --- /usr/bin/make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend --- Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake Scanning dependencies of target substructLibraryTest /usr/bin/make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build --- Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o --- [ 78%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp --- Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/all --- --- lib/libRDKitMMPA.so.1.2018.09.3 --- [ 78%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/MMPA.dir/MMPA.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MMPA && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2018.09.3 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so [ 78%] Built target MMPA --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 79%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp --- Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/all --- --- Code/GraphMol/Trajectory/trajectoryTest --- [ 80%] Linking CXX executable trajectoryTest cd /construction/science/rdkit/.build/Code/GraphMol/Trajectory && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 80%] Built target trajectoryTest --- Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/all --- /usr/bin/make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend --- Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolInterchange /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolInterchange /construction/science/rdkit/.build/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake Scanning dependencies of target molInterchangeTest1 /usr/bin/make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build --- Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o --- [ 80%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolInterchange && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/rapidjson-1.1.0/include -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolInterchange/test1.cpp --- Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Fingerprints.h:16, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/SubstructLibrary.h:39, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp:19: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/all --- In file included from /usr/local/include/boost/graph/adjacency_list.hpp:223, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ROMol.h:27, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/GraphMol.h:19, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/../RDKitBase.h:26, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/MaximumCommonSubgraph.h:15, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/Seed.cpp:10: /usr/local/include/boost/graph/detail/adjacency_list.hpp: In member function 'unsigned int RDKit::FMCS::Seed::addBond(const RDKit::Bond*)': /usr/local/include/boost/graph/detail/adjacency_list.hpp:2240:43: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] typename Config::edge_property_type p; ^ /usr/local/include/boost/graph/detail/adjacency_list.hpp: In member function 'void RDKit::FMCS::Seed::grow(RDKit::FMCS::MaximumCommonSubgraph&) const': /usr/local/include/boost/graph/detail/adjacency_list.hpp:2240:43: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] /usr/local/include/boost/graph/detail/adjacency_list.hpp:2240:43: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] /usr/local/include/boost/graph/detail/adjacency_list.hpp:2240:43: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o --- [ 80%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/bin/c++ -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp --- Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/all --- --- Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o --- [ 80%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp --- Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/all --- --- Code/GraphMol/SubstructLibrary/substructLibraryTest --- [ 80%] Linking CXX executable substructLibraryTest cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitSubstructLibrary.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 80%] Built target substructLibraryTest --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/rdmolfiles.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o --- [ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/PBF.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/PBF.cpp --- Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/all --- --- Code/GraphMol/MolInterchange/molInterchangeTest1 --- [ 80%] Linking CXX executable molInterchangeTest1 cd /construction/science/rdkit/.build/Code/GraphMol/MolInterchange && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitMolInterchange.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 80%] Built target molInterchangeTest1 --- Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/all --- /usr/bin/make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend --- Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MMPA /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MMPA /construction/science/rdkit/.build/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake Scanning dependencies of target testMMPA /usr/bin/make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build --- Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o --- [ 80%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MMPA && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MMPA/MMPA_UnitTest.cpp --- Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Fingerprints.h:16, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/SubstructLibrary.h:39, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:35: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/all --- In file included from /usr/local/include/boost/graph/adjacency_list.hpp:223, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ROMol.h:27, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/GraphMol.h:19, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RDKitBase.h:26, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/QueryOps.h:19, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/../QueryAtom.h:16, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp:13: /usr/local/include/boost/graph/detail/adjacency_list.hpp: In member function 'void RDKit::FMCS::RingMatchTableSet::makeRingGraph(RDKit::FMCS::Graph&, const INT_VECT&, const RDKit::ROMol*) const': /usr/local/include/boost/graph/detail/adjacency_list.hpp:2240:43: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] typename Config::edge_property_type p; ^ /usr/local/include/boost/graph/detail/adjacency_list.hpp: In member function 'void boost::vec_adj_list_impl::copy_impl(const boost::vec_adj_list_impl&) [with Graph = boost::adjacency_list; Config = boost::detail::adj_list_gen, boost::vecS, boost::vecS, boost::undirectedS, unsigned int, unsigned int, boost::no_property, boost::listS>::config; Base = boost::undirected_graph_helper, boost::vecS, boost::vecS, boost::undirectedS, unsigned int, unsigned int, boost::no_property, boost::listS>::config>]': /usr/local/include/boost/graph/detail/adjacency_list.hpp:2240:43: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] /usr/local/include/boost/graph/detail/adjacency_list.hpp: In member function 'void RDKit::FMCS::MaximumCommonSubgraph::init()': /usr/local/include/boost/graph/detail/adjacency_list.hpp:2240:43: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o --- [ 80%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/bin/c++ -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/SubstructMatchCustom.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o --- [ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/PMI.cpp --- Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/all --- --- lib/libRDKitFMCS.so.1.2018.09.3 --- [ 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 -std=c++11 -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.1.2018.09.3 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 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2018.09.3 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so [ 80%] Built target FMCS --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o --- [ 80%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp --- Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/all --- --- Code/GraphMol/MMPA/testMMPA --- [ 80%] Linking CXX executable testMMPA cd /construction/science/rdkit/.build/Code/GraphMol/MMPA && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitMMPA.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 80%] Built target testMMPA --- Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/all --- /usr/bin/make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend --- Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FMCS /construction/science/rdkit/.build/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake Scanning dependencies of target testFMCS /usr/bin/make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build --- Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o --- [ 80%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/testFMCS_Unit.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/rdmolfiles.cpp:13: /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&, T) [with T = int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = std::__cxx11::basic_string]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'RDKit::ROMol* RDKit::MolFromSmiles(boost::python::api::object, bool, boost::python::dict)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'RDKit::ROMol* RDKit::MolFromSmarts(boost::python::api::object, bool, boost::python::dict)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o --- [ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/AUTOCORR3D.cpp --- Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/all --- --- rdkit/Chem/rdSubstructLibrary.so --- [ 80%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 80%] Built target rdSubstructLibrary --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o --- [ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp --- Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/all --- 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp --- Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp:11: /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- rdkit/Chem/rdMMPA.so --- [ 80%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitMMPA.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 80%] Built target rdMMPA --- Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/all --- /usr/bin/make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend --- Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/Test /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/FMCS/Test /construction/science/rdkit/.build/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake Scanning dependencies of target FMCStest /usr/bin/make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build --- Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o --- [ 80%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/Test/testFMCS.cpp --- Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/all --- --- Code/GraphMol/FMCS/testFMCS --- [ 80%] Linking CXX executable testFMCS cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFMCS.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 80%] Built target testFMCS --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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++ -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o --- [ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/RDF.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:14: /usr/local/include/boost/python/extract.hpp: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o --- [ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/MaeMolSupplier.cpp --- Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:10: /usr/local/include/boost/python/extract.hpp: In function 'RDKit::MCSResult* RDKit::FindMCSWrapper2(boost::python::api::object, const RDKit::MCSParameters&)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'RDKit::MCSResult* RDKit::FindMCSWrapper(boost::python::api::object, bool, double, unsigned int, bool, bool, bool, bool, bool, RDKit::AtomComparator, RDKit::BondComparator, std::__cxx11::string)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o --- [ 82%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/MORSE.cpp --- Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/all --- --- rdkit/Chem/rdFMCS.so --- [ 82%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 82%] Built target rdFMCS --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o --- [ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/SDMolSupplier.cpp --- Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/all --- --- Code/GraphMol/FMCS/Test/FMCStest --- [ 82%] Linking CXX executable FMCStest cd /construction/science/rdkit/.build/Code/GraphMol/FMCS/Test && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../../lib/libRDKitFMCS.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 82%] Built target FMCStest --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o --- [ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/TDTMolSupplier.cpp --- Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/all --- --- lib/libRDKitRGroupDecomposition.so.1.2018.09.3 --- [ 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitFMCS.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2018.09.3 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so [ 82%] Built target RGroupDecomposition --- Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/all --- /usr/bin/make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend --- Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RGroupDecomposition /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o --- [ 82%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/GETAWAY.cpp --- Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/all --- Scanning dependencies of target testRGroupDecomp /usr/bin/make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build --- Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o --- [ 82%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/MaeMolSupplier.cpp:12: /usr/local/include/boost/python/extract.hpp: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o --- [ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/SmilesMolSupplier.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o --- [ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/SmilesWriter.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/SDMolSupplier.cpp:13: /usr/local/include/boost/python/extract.hpp: In function 'void RDKit::setStreamIndices(RDKit::SDMolSupplier&, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o --- [ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/SDWriter.cpp --- Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/all --- --- Code/GraphMol/RGroupDecomposition/testRGroupDecomp --- [ 82%] Linking CXX executable testRGroupDecomp cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitRGroupDecomposition.so.1.2018.09.3 ../../../lib/libRDKitFMCS.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 82%] Built target testRGroupDecomp --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- [ 82%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/SmilesWriter.cpp:12: /usr/local/include/boost/python/extract.hpp: In function 'void RDKit::SetSmiWriterProps(RDKit::SmilesWriter&, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/SDWriter.cpp:13: /usr/local/include/boost/python/extract.hpp: In function 'void RDKit::SetSDWriterProps(RDKit::SDWriter&, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o --- /usr/local/include/boost/python/extract.hpp: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o --- /usr/local/include/boost/python/extract.hpp: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o --- /usr/local/include/boost/python/extract.hpp: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o --- /usr/local/include/boost/python/extract.hpp: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o --- [ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/TDTWriter.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o --- [ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/PDBWriter.cpp --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o --- [ 82%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/WHIM.cpp --- Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp:32: /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector >; DerivedPolicies = boost::python::detail::final_vector_derived_policies >, true>; ProxyHandler = boost::python::detail::no_proxy_helper >, boost::python::detail::final_vector_derived_policies >, true>, boost::python::detail::container_element >, long unsigned int, boost::python::detail::final_vector_derived_policies >, true> >, long unsigned int>; Data = boost::shared_ptr; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ In file included from /usr/local/include/boost/shared_ptr.hpp:17, from /usr/local/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/local/include/boost/python/converter/arg_to_python.hpp:15, from /usr/local/include/boost/python/call.hpp:15, from /usr/local/include/boost/python/object_core.hpp:14, from /usr/local/include/boost/python/args.hpp:22, from /usr/local/include/boost/python.hpp:11, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp:32: /usr/local/include/boost/smart_ptr/shared_ptr.hpp: In function 'boost::python::api::object RDKit::RGroupDecomp(boost::python::api::object, boost::python::api::object, bool, bool, const RDKit::RGroupDecompositionParameters&)': /usr/local/include/boost/smart_ptr/shared_ptr.hpp:422:66: warning: '*((void*)(&)+32).boost::shared_ptr::px' may be used uninitialized in this function [-Wmaybe-uninitialized] shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) ~~^~ In file included from /usr/local/include/boost/smart_ptr/shared_ptr.hpp:28, from /usr/local/include/boost/shared_ptr.hpp:17, from /usr/local/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/local/include/boost/python/converter/arg_to_python.hpp:15, from /usr/local/include/boost/python/call.hpp:15, from /usr/local/include/boost/python/object_core.hpp:14, from /usr/local/include/boost/python/args.hpp:22, from /usr/local/include/boost/python.hpp:11, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp:32: /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:433:67: warning: '*((void*)(&)+40).boost::detail::shared_count::pi_' may be used uninitialized in this function [-Wmaybe-uninitialized] shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) ~~^~~ In file included from /usr/local/include/boost/shared_ptr.hpp:17, from /usr/local/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/local/include/boost/python/converter/arg_to_python.hpp:15, from /usr/local/include/boost/python/call.hpp:15, from /usr/local/include/boost/python/object_core.hpp:14, from /usr/local/include/boost/python/args.hpp:22, from /usr/local/include/boost/python.hpp:11, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp:32: /usr/local/include/boost/smart_ptr/shared_ptr.hpp:422:66: warning: '*((void*)(&)+32).boost::shared_ptr::px' may be used uninitialized in this function [-Wmaybe-uninitialized] shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) ~~^~ In file included from /usr/local/include/boost/smart_ptr/shared_ptr.hpp:28, from /usr/local/include/boost/shared_ptr.hpp:17, from /usr/local/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/local/include/boost/python/converter/arg_to_python.hpp:15, from /usr/local/include/boost/python/call.hpp:15, from /usr/local/include/boost/python/object_core.hpp:14, from /usr/local/include/boost/python/args.hpp:22, from /usr/local/include/boost/python.hpp:11, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp:32: /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:433:67: warning: '*((void*)(&)+40).boost::detail::shared_count::pi_' may be used uninitialized in this function [-Wmaybe-uninitialized] shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) ~~^~~ --- rdkit/Chem/rdRGroupDecomposition.so --- [ 82%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitFMCS.so.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 82%] Built target rdRGroupDecomposition --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/PDBWriter.cpp:12: /usr/local/include/boost/python/extract.hpp: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/TDTWriter.cpp:13: /usr/local/include/boost/python/extract.hpp: In function 'void RDKit::SetTDTWriterProps(RDKit::TDTWriter&, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- rdkit/Chem/rdmolfiles.so --- [ 83%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 83%] Built target rdmolfiles --- Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/all --- --- lib/libRDKitDescriptors.so.1.2018.09.3 --- [ 83%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o 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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so [ 83%] Built target Descriptors --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/all --- /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend --- Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/all --- /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend --- 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/CMakeFiles/testDescriptors.dir/all --- /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend --- Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/all --- /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend --- Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Descriptors /construction/science/rdkit/.build/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend --- --- Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend --- --- Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend --- --- Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Descriptors /construction/science/rdkit/.build/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/DependInfo.cmake --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/Descriptors/CMakeFiles/testAUTOCORR2D.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Descriptors /construction/science/rdkit/.build/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake --- Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Descriptors /construction/science/rdkit/.build/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake --- Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/all --- Scanning dependencies of target testRDFcustom /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build --- Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o --- [ 83%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/testRDFcustom.cpp --- Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/all --- Scanning dependencies of target testPBF /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build --- Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/all --- Scanning dependencies of target testAUTOCORR2D /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build --- Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o --- [ 83%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testPBF.dir/testPBF.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/testPBF.cpp --- Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/all --- --- Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o --- [ 83%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp --- Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/all --- Scanning dependencies of target testDescriptors /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build --- Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o --- [ 83%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/test.cpp --- 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 --- [ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/Reaction.cpp --- Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/test.cpp:24: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/all --- --- Code/GraphMol/Descriptors/testAUTOCORR2D --- [ 83%] Linking CXX executable testAUTOCORR2D cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 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Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Descriptors /construction/science/rdkit/.build/Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/DependInfo.cmake Scanning dependencies of target testWHIM /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build --- Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o --- [ 83%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Descriptors /construction/science/rdkit/.build/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake Scanning dependencies of target testRDF /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build --- Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o --- [ 83%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m 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/construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Descriptors /construction/science/rdkit/.build/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake Scanning dependencies of target testMORSE /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build --- Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o --- [ 83%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/testMORSE.cpp --- Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/all --- --- Code/GraphMol/Descriptors/testWHIM --- [ 83%] Linking CXX executable testWHIM cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testWHIM.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 83%] Built target testWHIM --- Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/all --- /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend --- Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Descriptors /construction/science/rdkit/.build/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake Scanning dependencies of target test3D /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build --- Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o --- [ 84%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/test3D.dir/test3D.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/test3D.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/MDLParser.cpp:39: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/all --- --- Code/GraphMol/Descriptors/testMORSE --- [ 84%] Linking CXX executable testMORSE cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMORSE.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMORSE.dir/testMORSE.cpp.o -o testMORSE -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 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/construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Descriptors /construction/science/rdkit/.build/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake Scanning dependencies of target testEEM /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build --- Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o --- [ 84%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 84%] Built target testRDF --- Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/all --- /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/depend --- Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Descriptors /construction/science/rdkit/.build/Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/DependInfo.cmake Scanning dependencies of target testGETAWAY /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build --- Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o --- [ 84%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/testGETAWAY.cpp --- Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/test3D.cpp:29: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. 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-I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/DaylightParser.cpp --- Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/all --- --- Code/GraphMol/Descriptors/testDescriptors --- [ 84%] Linking CXX executable testDescriptors cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 84%] Built target testDescriptors --- Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/all --- /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend --- Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/Descriptors /construction/science/rdkit/.build/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake Scanning dependencies of target testAUTOCORR3D /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/testAUTOCORR3D.cpp --- Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/all --- --- Code/GraphMol/Descriptors/test3D --- [ 84%] Linking CXX executable test3D cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/test3D.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/test3D.dir/test3D.cpp.o -o test3D -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 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Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/Descriptors/CMakeFiles/testGETAWAY.dir/all --- --- Code/GraphMol/Descriptors/testGETAWAY --- [ 84%] Linking CXX executable testGETAWAY cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testGETAWAY.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -o testGETAWAY -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 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Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/all --- --- Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o --- --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o --- --- Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/all --- [ 84%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolAlign/testMolAlign.cpp --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- [ 84%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDescriptors_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp --- Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/all --- --- Code/GraphMol/Descriptors/testEEM --- [ 84%] Linking CXX executable testEEM cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testEEM.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testEEM.dir/testEEM.cpp.o -o testEEM -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 84%] Built target testEEM --- 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/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 84%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp --- Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/all --- --- Code/GraphMol/Descriptors/testAUTOCORR3D --- [ 84%] Linking CXX executable testAUTOCORR3D cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 84%] Built target testAUTOCORR3D --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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/MolHash.cpp.o --- [ 84%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/MolHash.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolHash && /usr/bin/c++ -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolHash.dir/MolHash.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolHash/MolHash.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/ReactionPickler.cpp:18: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/AtomPairs.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:19: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- 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++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/ReactionWriter.cpp --- Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/all --- --- Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/HashToString.cpp.o --- [ 84%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/HashToString.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolHash && /usr/bin/c++ -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolHash.dir/HashToString.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolHash/HashToString.cpp --- Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/all --- --- Code/GraphMol/MolAlign/testMolAlign --- [ 84%] Linking CXX executable testMolAlign cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.3 ../../../lib/libRDKitDistGeometry.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 84%] Built target testMolAlign --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- /usr/bin/make -f Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/depend --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/StructChecker /construction/science/rdkit/.build/Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/DependInfo.cmake --- Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:14: /usr/local/include/boost/python/extract.hpp: In member function 'unsigned int PySequenceHolder::size() const [with T = boost::python::api::object]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In member function 'unsigned int PySequenceHolder::size() const [with T = int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In member function 'unsigned int PySequenceHolder::size() const [with T = double]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In member function 'unsigned int PySequenceHolder::size() const [with T = unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- 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++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/ReactionDepict.cpp --- Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/all --- /usr/local/include/boost/python/extract.hpp: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'RDKit::MatchVectType* RDKit::_translateAtomMap(boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'RDNumeric::DoubleVector* RDKit::_translateWeights(boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- Scanning dependencies of target StructChecker /usr/bin/make -f Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructChecker.cpp.o --- [ 84%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructChecker.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/StructChecker.dir/StructChecker.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/StructChecker.cpp --- Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/all --- /usr/local/include/boost/python/extract.hpp: In function 'std::vector* RDKit::_translateIds(boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'std::vector > > RDKit::_translateAtomMapVector(boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- rdkit/Chem/rdMolAlign.so --- [ 84%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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/libRDKitDescriptors.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 84%] Built target rdMolAlign --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o --- [ 84%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/StructCheckerOptions.cpp --- Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/all --- --- lib/libRDKitMolHash.so.1.2018.09.3 --- [ 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/MolHash.dir/MolHash.cpp.o CMakeFiles/MolHash.dir/HashToString.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MolHash && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2018.09.3 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so [ 85%] Built target MolHash --- Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/all --- /usr/bin/make -f Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/depend --- Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolHash /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolHash /construction/science/rdkit/.build/Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/DependInfo.cmake Scanning dependencies of target testMolHash /usr/bin/make -f Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build --- Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/testMolHash.cpp.o --- [ 85%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/testMolHash.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolHash && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testMolHash.dir/testMolHash.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolHash/testMolHash.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o --- [ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/Wrap.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:10: /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::CalcCustomPropVSA(const RDKit::ROMol&, std::__cxx11::string, boost::python::api::object, bool)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::CalcPEOEVSA(const RDKit::ROMol&, boost::python::api::object, bool)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::CalcSMRVSA(const RDKit::ROMol&, boost::python::api::object, bool)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::CalcSlogPVSA(const RDKit::ROMol&, boost::python::api::object, bool)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructureFlags.cpp.o --- [ 87%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructureFlags.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/StructChecker.dir/StructureFlags.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/StructureFlags.cpp --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- /usr/local/include/boost/python/extract.hpp: In function 'double {anonymous}::GetUSRScore(boost::python::api::object, boost::python::api::object, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::GetUSRDistributionsFromPoints(boost::python::api::object, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ In file included from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Conformer.h:14, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ROMol.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/GraphMol.h:19, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:12: /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/point.h:85:15: warning: '*((void*)(&)+32).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] x = other.x; ~~~~~~^ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/point.h:86:15: warning: '*((void*)(&)+32).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] y = other.y; ~~~~~~^ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/point.h:87:15: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] z = other.z; ~~~~~~^ In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/Wrap.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:10: /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::GetUSRDistributions(boost::python::api::object, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ In file included from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Conformer.h:14, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ROMol.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/GraphMol.h:19, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:12: /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/point.h:85:15: warning: '*((void*)(&)+32).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] x = other.x; ~~~~~~^ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/point.h:86:15: warning: '*((void*)(&)+32).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] y = other.y; ~~~~~~^ /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/point.h:87:15: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] z = other.z; ~~~~~~^ In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/Wrap.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:10: /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::GetUSRCAT(const RDKit::ROMol&, boost::python::api::object, int)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/../../RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/StructCheckerOptions.cpp:17: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- /usr/local/include/boost/python/extract.hpp: In function 'RDKit::SparseIntVect* {anonymous}::{anonymous}::MorganFingerprintHelper(const RDKit::ROMol&, int, int, boost::python::api::object, boost::python::api::object, bool, bool, bool, bool, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&, T) [with T = unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'ExplicitBitVect* {anonymous}::GetMorganFingerprintBV(const RDKit::ROMol&, int, unsigned int, boost::python::api::object, boost::python::api::object, bool, bool, bool, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::GetUSRFromDistributions(boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::list {anonymous}::computeCrippenContribs(const RDKit::ROMol&, bool, boost::python::list, boost::python::list)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Fingerprints.h:16, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp:37: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o --- --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Utilites.cpp.o --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- [ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/ReactionUtils.cpp --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- [ 87%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Utilites.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/StructChecker.dir/Utilites.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/Utilites.cpp --- Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/all --- --- Code/GraphMol/MolHash/testMolHash --- [ 87%] Linking CXX executable testMolHash cd /construction/science/rdkit/.build/Code/GraphMol/MolHash && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testMolHash.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testMolHash.dir/testMolHash.cpp.o -o testMolHash -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitMolHash.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 87%] Built target testMolHash --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 87%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Pattern.cpp.o --- [ 87%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Pattern.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/StructChecker.dir/Pattern.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/Pattern.cpp--- Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/all --- --- rdkit/Chem/rdMolDescriptors.so --- [ 88%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 88%] Built target rdMolDescriptors --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o --- [ 88%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/MoleculeParser.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o --- [ 88%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/ReactionRunner.cpp --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Stereo.cpp.o --- [ 88%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Stereo.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/StructChecker.dir/Stereo.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/Stereo.cpp --- Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp:10: /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&, T) [with T = unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- rdkit/Chem/rdMolHash.so --- [ 88%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 88%] Built target rdMolHash --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/AtomSymbolMatch.cpp.o --- [ 88%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/AtomSymbolMatch.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/StructChecker.dir/AtomSymbolMatch.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/AtomSymbolMatch.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o --- [ 88%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/PreprocessRxn.cpp --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StripSmallFragments.cpp.o --- [ 88%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StripSmallFragments.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/StructChecker.dir/StripSmallFragments.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/StripSmallFragments.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/PreprocessRxn.cpp:39: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/ReCharge.cpp.o --- [ 88%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/ReCharge.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/StructChecker.dir/ReCharge.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/ReCharge.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o --- [ 88%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/SanitizeRxn.cpp --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Tautomer.cpp.o --- [ 88%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Tautomer.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/StructChecker.dir/Tautomer.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/Tautomer.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o --- [ 88%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o --- [ 88%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o --- [ 89%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp --- Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/all --- --- lib/libRDKitStructChecker.so.1.2018.09.3 --- [ 90%] Linking CXX shared library ../../../lib/libRDKitStructChecker.so cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/StructChecker.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitStructChecker.so.1 -o ../../../lib/libRDKitStructChecker.so.1.2018.09.3 CMakeFiles/StructChecker.dir/StructChecker.cpp.o CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o CMakeFiles/StructChecker.dir/StructureFlags.cpp.o CMakeFiles/StructChecker.dir/Utilites.cpp.o CMakeFiles/StructChecker.dir/Pattern.cpp.o CMakeFiles/StructChecker.dir/Stereo.cpp.o CMakeFiles/StructChecker.dir/AtomSymbolMatch.cpp.o CMakeFiles/StructChecker.dir/StripSmallFragments.cpp.o CMakeFiles/StructChecker.dir/ReCharge.cpp.o CMakeFiles/StructChecker.dir/Tautomer.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitStructChecker.so.1.2018.09.3 ../../../lib/libRDKitStructChecker.so.1 ../../../lib/libRDKitStructChecker.so [ 90%] Built target StructChecker --- Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/all --- /usr/bin/make -f Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/depend --- Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/StructChecker /construction/science/rdkit/.build/Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/DependInfo.cmake Scanning dependencies of target testStructChecker /usr/bin/make -f Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build --- Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/testStructChecker.cpp.o --- [ 90%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/testStructChecker.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testStructChecker.dir/testStructChecker.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/testStructChecker.cpp --- Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/all --- /usr/bin/make -f Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build.make Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/depend --- Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/StructChecker/Wrap /construction/science/rdkit/.build/Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/DependInfo.cmake Scanning dependencies of target rdStructChecker /usr/bin/make -f Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build.make Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build --- Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/structchecker.cpp.o --- [ 90%] Building CXX object Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/structchecker.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdStructChecker_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdStructChecker.dir/structchecker.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/Wrap/structchecker.cpp --- Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/all --- --- Code/GraphMol/StructChecker/testStructChecker --- [ 90%] Linking CXX executable testStructChecker cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testStructChecker.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testStructChecker.dir/testStructChecker.cpp.o -o testStructChecker -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib ../../../lib/libRDKitStructChecker.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- --- lib/libRDKitChemReactions.so.1.2018.09.3 --- [ 90%] 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 -std=c++11 -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.1.2018.09.3 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/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.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread --- Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/all --- [ 90%] Built target testStructChecker --- Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all --- cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so [ 90%] Built target ChemReactions --- Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all --- /usr/bin/make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend --- Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/all --- /usr/bin/make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend --- Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/all --- /usr/bin/make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend --- Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/all --- /usr/bin/make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend --- Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend --- --- Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend --- --- Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend --- --- Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/all --- --- Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend --- --- Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ChemReactions /construction/science/rdkit/.build/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --- Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ChemReactions /construction/science/rdkit/.build/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --- Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ChemReactions /construction/science/rdkit/.build/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --- Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/ChemReactions /construction/science/rdkit/.build/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --- Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/all --- Scanning dependencies of target testEnumeration --- Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all --- Scanning dependencies of target testReaction /usr/bin/make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build --- Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o --- [ 90%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/testReaction.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/all --- Scanning dependencies of target testReactionFingerprints /usr/bin/make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build --- Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o --- [ 90%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/all --- /usr/bin/make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build --- Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o --- [ 91%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/all --- Scanning dependencies of target rxnTestCatch /usr/bin/make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build --- Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o --- [ 91%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/bin/c++ -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/catch_tests.cpp --- Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/all --- --- rdkit/Chem/rdStructChecker.so --- [ 91%] Linking CXX shared module ../../../../rdkit/Chem/rdStructChecker.so cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdStructChecker.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o ../../../../rdkit/Chem/rdStructChecker.so CMakeFiles/rdStructChecker.dir/structchecker.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitStructChecker.so.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 91%] Built target rdStructChecker --- 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/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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 91%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/ReactionFingerprints.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp:41: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/ChemReactions/testReactionFingerprints --- [ 92%] Linking CXX executable testReactionFingerprints cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 92%] Built target testReactionFingerprints --- 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/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 Scanning dependencies of target MolDraw2D /usr/bin/make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o --- [ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/all --- --- Code/GraphMol/ChemReactions/testEnumeration --- [ 92%] Linking CXX executable testEnumeration cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 92%] Built target testEnumeration --- 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/MolStandardize/CMakeFiles/MolStandardize.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 Scanning dependencies of target MolStandardize /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o --- [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/MolStandardize.cpp In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Normalize.h:19, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/MolStandardize.cpp:12: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o --- [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Metal.cpp --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/local/include/boost/python/extract.hpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector > >; DerivedPolicies = boost::python::detail::final_vector_derived_policies > >, false>; ProxyHandler = boost::python::detail::proxy_helper > >, boost::python::detail::final_vector_derived_policies > >, false>, boost::python::detail::container_element > >, long unsigned int, boost::python::detail::final_vector_derived_policies > >, false> >, long unsigned int>; Data = std::vector >; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = long unsigned int; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector > >; DerivedPolicies = boost::python::detail::final_vector_derived_policies > >, false>; ProxyHandler = boost::python::detail::proxy_helper > >, boost::python::detail::final_vector_derived_policies > >, false>, boost::python::detail::container_element > >, long unsigned int, boost::python::detail::final_vector_derived_policies > >, false> >, long unsigned int>; Data = std::vector >; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o --- [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Normalize.cpp --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o --- [ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/all --- --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o --- [ 92%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Normalize.h:19, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Normalize.cpp:10: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h:36, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:42: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o --- [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Validate.cpp --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp --- Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/all --- --- Code/GraphMol/ChemReactions/rxnTestCatch --- [ 94%] Linking CXX executable rxnTestCatch cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 [ 94%] Built target rxnTestCatch --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Charge.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Fragment.h:14, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Validate.cpp:11: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Charge.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Charge.cpp:10: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Tautomer.cpp --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/all --- In file included from /usr/local/include/boost/shared_ptr.hpp:17, from /usr/local/include/boost/smart_ptr.hpp:19, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics/Vector.h:23, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/point.h:24, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolPickler.h:14, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:32: /usr/local/include/boost/smart_ptr/shared_ptr.hpp: In function 'PyObject* RDKit::RunReactant(RDKit::ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]': /usr/local/include/boost/smart_ptr/shared_ptr.hpp:422:66: warning: '*((void*)(&)+32).boost::shared_ptr::px' may be used uninitialized in this function [-Wmaybe-uninitialized] shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) ~~^~ In file included from /usr/local/include/boost/smart_ptr/shared_ptr.hpp:28, from /usr/local/include/boost/shared_ptr.hpp:17, from /usr/local/include/boost/smart_ptr.hpp:19, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Numerics/Vector.h:23, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Geometry/point.h:24, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolPickler.h:14, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:32: /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:433:67: warning: '*((void*)(&)+40).boost::detail::shared_count::pi_' may be used uninitialized in this function [-Wmaybe-uninitialized] shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) ~~^~~ --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Tautomer.h:15, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Tautomer.cpp:10: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Fragment.cpp --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/props.hpp:34, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:33: /usr/local/include/boost/python/extract.hpp: In function 'PyObject* RDKit::RunReactants(RDKit::ChemicalReaction*, T, unsigned int) [with T = boost::python::tuple]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'PyObject* RDKit::RunReactants(RDKit::ChemicalReaction*, T, unsigned int) [with T = boost::python::list]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'RDKit::ChemicalReaction* RDKit::ReactionFromSmarts(const char*, boost::python::dict, bool)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::api::object RDKit::PreprocessReaction(RDKit::ChemicalReaction&, boost::python::dict, std::__cxx11::string)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::api::object RDKit::AddRecursiveQueriesToReaction(RDKit::ChemicalReaction&, boost::python::dict, std::__cxx11::string, bool)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector >; DerivedPolicies = boost::python::detail::final_vector_derived_policies >, true>; ProxyHandler = boost::python::detail::no_proxy_helper >, boost::python::detail::final_vector_derived_policies >, true>, boost::python::detail::container_element >, long unsigned int, boost::python::detail::final_vector_derived_policies >, true> >, long unsigned int>; Data = boost::shared_ptr; Index = long unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp --- Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/all --- --- lib/libRDKitMolDraw2D.so.1.2018.09.3 --- [ 94%] 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /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.1.2018.09.3 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so [ 94%] Built target MolDraw2D --- Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/all --- /usr/bin/make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend --- Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolDraw2D /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Fragment.h:14, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Fragment.cpp:10: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/all --- Scanning dependencies of target moldraw2DTest1 /usr/bin/make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build --- Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolDraw2D/test1.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp:15: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/all --- --- rdkit/Chem/rdChemReactions.so --- --- Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all --- --- Code/GraphMol/ChemReactions/testReaction --- [ 94%] Linking CXX executable testReaction cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 --- Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/all --- [ 94%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 94%] Built target rdChemReactions --- Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/all --- /usr/bin/make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend --- Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolDraw2D /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --- Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all --- [ 94%] Built target testReaction --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 --- Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/all --- Scanning dependencies of target moldraw2DRxnTest1 /usr/bin/make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build --- Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolDraw2D/rxn_test1.cpp --- Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/all --- 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 --- [ 94%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o --- [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o --- [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o --- [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp:15: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/all --- --- Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 --- [ 96%] Linking CXX executable moldraw2DRxnTest1 cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolDraw2D.so.1.2018.09.3 ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 96%] Built target moldraw2DRxnTest1 --- 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/rdmolops.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o --- [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp --- Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/all --- --- Code/GraphMol/MolDraw2D/moldraw2DTest1 --- [ 96%] Linking CXX executable moldraw2DTest1 cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolDraw2D.so.1.2018.09.3 ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 96%] Built target moldraw2DTest1 --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/all --- --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o --- [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/MolOps.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o --- [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp:15: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o --- [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Fingerprints.h:16, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/MolOps.cpp:26: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: /usr/local/include/boost/python/extract.hpp: In static member function 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::map >; DerivedPolicies = boost::python::detail::final_map_derived_policies >, true>; bool NoProxy = true; bool NoSlice = true; Data = std::__cxx11::basic_string; Index = int; Key = int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& x +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o --- [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o --- [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp --- Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/all --- /usr/local/include/boost/python/extract.hpp: In static member function 'static boost::python::api::object boost::python::indexing_suite::base_get_item(boost::python::back_reference, PyObject*) [with Container = std::map >; DerivedPolicies = boost::python::detail::final_map_derived_policies >, true>; bool NoProxy = true; bool NoSlice = true; Data = std::__cxx11::basic_string; Index = int; Key = int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& i +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static void boost::python::indexing_suite::base_delete_item(Container&, PyObject*) [with Container = std::map >; DerivedPolicies = boost::python::detail::final_map_derived_policies >, true>; bool NoProxy = true; bool NoSlice = true; Data = std::__cxx11::basic_string; Index = int; Key = int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& i +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'void pythonObjectToVect(const boost::python::api::object&, std::vector&) [with T = int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = RDKit::ROMol*]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'RDKit::DrawColour RDKit::{anonymous}::pyTupleToDrawColour(boost::python::tuple)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'void RDKit::drawReactionHelper(RDKit::MolDraw2D&, const RDKit::ChemicalReaction&, bool, boost::python::api::object, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&, T) [with T = int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = std::__cxx11::basic_string]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'void RDKit::{anonymous}::pyDictToColourMap(boost::python::api::object, RDKit::ColourPalette&)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp:15: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/all --- /usr/local/include/boost/python/extract.hpp: In function 'void RDKit::{anonymous}::pyDictToDoubleMap(boost::python::api::object, std::map&)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'void RDKit::drawMoleculesHelper2(RDKit::MolDraw2D&, boost::python::api::object, boost::python::api::object, boost::python::api::object, boost::python::api::object, boost::python::api::object, boost::python::api::object, boost::python::api::object, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In static member function 'static boost::python::map_indexing_suite::index_type boost::python::map_indexing_suite::convert_index(Container&, PyObject*) [with Container = std::map >; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_map_derived_policies >, true>]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& i +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o --- [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o --- [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp --- Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/all --- --- rdkit/Chem/Draw/rdMolDraw2D.so --- [ 97%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/local/lib/libboost_serialization.so [ 97%] Built target rdMolDraw2D --- Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/all --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/python.h:3, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/Wrap/MolOps.cpp:12: /usr/local/include/boost/python/extract.hpp: In function 'boost::python::dict RDKit::splitMolByPDBChainId(const RDKit::ROMol&, boost::python::api::object, bool)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::dict RDKit::splitMolByPDBResidues(const RDKit::ROMol&, boost::python::api::object, bool)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'RDKit::ROMol* RDKit::pathToSubmolHelper(const RDKit::ROMol&, boost::python::api::object&, bool, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'ExplicitBitVect* RDKit::wrapPatternFingerprint(const RDKit::ROMol&, unsigned int, boost::python::list, ExplicitBitVect*)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&, T) [with T = int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&, T) [with T = unsigned int]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'boost::python::tuple RDKit::fragmentOnSomeBondsHelper(const RDKit::ROMol&, boost::python::api::object, unsigned int, bool, boost::python::api::object, boost::python::api::object, bool)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'RDKit::ROMol* RDKit::fragmentOnBondsHelper(const RDKit::ROMol&, boost::python::api::object, bool, boost::python::api::object, boost::python::api::object, boost::python::list)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'ExplicitBitVect* RDKit::wrapLayeredFingerprint(const RDKit::ROMol&, unsigned int, unsigned int, unsigned int, unsigned int, boost::python::list, ExplicitBitVect*, bool, boost::python::api::object)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'RDKit::ROMol* RDKit::replaceCoreHelper(const RDKit::ROMol&, const RDKit::ROMol&, boost::python::api::object, bool, bool, bool)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'void RDKit::addRecursiveQueriesHelper(RDKit::ROMol&, boost::python::dict, std::__cxx11::string)': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/all --- --- lib/libRDKitMolStandardize.so.1.2018.09.3 --- [ 97%] 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 -std=c++11 -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.1.2018.09.3 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.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /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.1.2018.09.3 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so [ 97%] Built target MolStandardize --- Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/all --- /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend --- Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/all --- /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend --- Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/all --- /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend --- Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/all --- /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend --- Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolStandardize /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake --- Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend --- --- Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend --- --- Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolStandardize /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --- Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend --- --- Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolStandardize /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --- Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/all --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolStandardize /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake --- Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/all --- Scanning dependencies of target molTautomerTest /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build --- Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/all --- Scanning dependencies of target molNormalizeTest /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build --- Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/all --- Scanning dependencies of target molChargeTest --- Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o --- --- Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o --- [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/testNormalize.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/all --- /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build --- Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/all --- [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/testTautomer.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/all --- --- Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o --- [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/testCharge.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/all --- Scanning dependencies of target molValidateTest /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build --- Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o --- [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/testValidate.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Tautomer.h:15, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/testTautomer.cpp:10: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Charge.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/testCharge.cpp:13: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Normalize.h:19, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/testNormalize.cpp:12: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolDraw2D.so.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/local/lib/libboost_serialization.so [ 97%] Built target rdmolops --- Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/all --- /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend --- Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolStandardize /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake Scanning dependencies of target molFragmentTest /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build --- Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o --- [ 98%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/testFragment.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/all --- --- Code/GraphMol/MolStandardize/molNormalizeTest --- [ 98%] Linking CXX executable molNormalizeTest cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolStandardize.so.1.2018.09.3 ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 98%] Built target molNormalizeTest --- Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/all --- /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend --- Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolStandardize /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake Scanning dependencies of target molStandardizeTest /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build --- Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o --- [ 98%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/test1.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/all --- --- Code/GraphMol/MolStandardize/molChargeTest --- [ 98%] Linking CXX executable molChargeTest cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolStandardize.so.1.2018.09.3 ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 98%] Built target molChargeTest --- Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/all --- /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend --- Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/GraphMol/MolStandardize /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake Scanning dependencies of target molStandardizeSmallTest /usr/bin/make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build --- Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o --- [ 98%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -pthread -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/test2.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/all --- --- Code/GraphMol/MolStandardize/molValidateTest --- [ 98%] Linking CXX executable molValidateTest cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolStandardize.so.1.2018.09.3 ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 98%] Built target molValidateTest --- 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/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend --- cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 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 --- [ 98%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Fragment.h:14, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/testFragment.cpp:13: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/all --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Normalize.h:19, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/test2.cpp:15: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/all --- --- Code/GraphMol/MolStandardize/molFragmentTest --- [ 98%] Linking CXX executable molFragmentTest cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolStandardize.so.1.2018.09.3 ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/local/lib/libboost_serialization.so [ 98%] Built target molFragmentTest --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o --- [ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/all --- --- Code/GraphMol/MolStandardize/molStandardizeSmallTest --- [ 99%] Linking CXX executable molStandardizeSmallTest cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolStandardize.so.1.2018.09.3 ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 99%] Built target molStandardizeSmallTest --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o --- [ 99%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/all --- --- Code/GraphMol/MolStandardize/molStandardizeTest --- [ 99%] Linking CXX executable molStandardizeTest cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolStandardize.so.1.2018.09.3 ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [ 99%] Built target molStandardizeTest --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o --- [ 99%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o --- [100%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp --- Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/all --- --- Code/GraphMol/MolStandardize/molTautomerTest --- [100%] Linking CXX executable molTautomerTest cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../lib/libRDKitMolStandardize.so.1.2018.09.3 ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread [100%] Built target molTautomerTest --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/all --- --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o --- [100%] 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++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/local/include/catch2 -I/construction/science/rdkit/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/construction/science/rdkit/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -fPIC -pthread -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Charge.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp:13: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Normalize.h:19, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp:13: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o --- In file included from /usr/local/include/boost/python/override.hpp:13, from /usr/local/include/boost/python/wrapper.hpp:8, from /usr/local/include/boost/python/object/value_holder.hpp:15, from /usr/local/include/boost/python/object/class_metadata.hpp:14, from /usr/local/include/boost/python/class.hpp:23, from /usr/local/include/boost/python.hpp:18, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDBoost/Wrap.h:20, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp:10: /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = boost::shared_ptr]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ /usr/local/include/boost/python/extract.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = RDKit::Atom*]': /usr/local/include/boost/python/extract.hpp:185:11: warning: '*((void*)& +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] ); ^ --- Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o --- In file included from /usr/local/include/boost/detail/endian.hpp:9, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/Catalogs/Catalog.h:29, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Fragment.h:14, from /construction/science/rdkit/rdkit-Release_2018_09_3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp:13: /usr/local/include/boost/predef/detail/endian_compat.h:11:161: note: #pragma message: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include and use BOOST_ENDIAN_*_BYTE instead") ^ --- rdkit/Chem/MolStandardize/rdMolStandardize.so --- [100%] 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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 -Wl,-z,origin,-rpath,/construction/science/rdkit/.build/lib:/usr/local/lib ../../../../lib/libRDKitMolStandardize.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/local/lib/libboost_serialization.so [100%] Built target rdMolStandardize /usr/local/bin/cmake -E cmake_progress_start /construction/science/rdkit/.build/CMakeFiles 0 -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> rdkit-2018.09.3_2 depends on package: py36-numpy>0 - found ===> rdkit-2018.09.3_2 depends on package: py36-matplotlib>0 - not found ===> Installing existing package /packages/All/py36-matplotlib-2.2.4.txz Installing py36-matplotlib-2.2.4... `-- Installing fontconfig-2.12.6,1... | `-- Installing freetype2-2.10.0... | `-- Extracting freetype2-2.10.0: .......... done `-- Extracting fontconfig-2.12.6,1: .......... done Running fc-cache to build fontconfig cache... /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 png-1.6.37... `-- Extracting png-1.6.37: .......... done `-- Installing py36-cycler-0.10.0... | `-- Installing py36-six-1.12.0... | `-- Extracting py36-six-1.12.0: .......... done `-- Extracting py36-cycler-0.10.0: .......... done `-- Installing py36-dateutil-2.8.0... `-- Extracting py36-dateutil-2.8.0: .......... done `-- Installing py36-kiwisolver-1.1.0... `-- Extracting py36-kiwisolver-1.1.0: ......... done `-- Installing py36-pyparsing-2.4.0... `-- Extracting py36-pyparsing-2.4.0: .......... done `-- Installing py36-pytz-2019.1,1... `-- Extracting py36-pytz-2019.1,1: .......... done `-- Installing py36-tkinter-3.6.9_6... | `-- Installing tcl86-8.6.9_1... | `-- Extracting tcl86-8.6.9_1: .......... done | `-- Installing tk86-8.6.9_1... | | `-- Installing libX11-1.6.8,1... | | `-- Installing libXau-1.0.9... | | `-- Extracting libXau-1.0.9: .......... done | | `-- Installing libXdmcp-1.1.3... | | | `-- Installing xorgproto-2019.1... | | | `-- Extracting xorgproto-2019.1: .......... done | | `-- Extracting libXdmcp-1.1.3: ......... done | | `-- Installing libxcb-1.13.1... | | | `-- Installing libpthread-stubs-0.4... | | | `-- Extracting libpthread-stubs-0.4: .... done | | | `-- Installing libxml2-2.9.9... | | | `-- Extracting libxml2-2.9.9: .......... done | | `-- Extracting libxcb-1.13.1: .......... done | | `-- Extracting libX11-1.6.8,1: .......... done | | `-- Installing libXScrnSaver-1.2.3_2... | | `-- Installing libXext-1.3.4,1... | | `-- Extracting libXext-1.3.4,1: .......... done | | `-- Extracting libXScrnSaver-1.2.3_2: .......... done | | `-- Installing libXft-2.3.2_3... | | `-- Installing libXrender-0.9.10_2... | | `-- Extracting libXrender-0.9.10_2: .......... done | | `-- Extracting libXft-2.3.2_3: .......... done | `-- Extracting tk86-8.6.9_1: .......... done `-- Extracting py36-tkinter-3.6.9_6: ........ done `-- Installing py36-tornado-5.1.1... `-- Extracting py36-tornado-5.1.1: .......... done Extracting py36-matplotlib-2.2.4: .......... done Message from freetype2-2.10.0: 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. 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). ===> rdkit-2018.09.3_2 depends on package: py36-matplotlib>0 - found ===> Returning to build of rdkit-2018.09.3_2 ===> rdkit-2018.09.3_2 depends on package: py36-pillow>0 - not found ===> Installing existing package /packages/All/py36-pillow-6.0.0_1.txz Installing py36-pillow-6.0.0_1... `-- Installing jpeg-turbo-2.0.2... `-- Extracting jpeg-turbo-2.0.2: .......... done `-- Installing openjpeg-2.3.1... | `-- Installing lcms2-2.9... | | `-- Installing tiff-4.0.10_1... | | `-- Installing jbigkit-2.1_1... | | `-- Extracting jbigkit-2.1_1: .......... done | | `-- Extracting tiff-4.0.10_1: .......... done | `-- Extracting lcms2-2.9: .......... done `-- Extracting openjpeg-2.3.1: .......... done `-- Installing py36-olefile-0.46... `-- Extracting py36-olefile-0.46: .......... done 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-------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for rdkit-2018.09.3_2 ===> Generating temporary packing list /usr/local/bin/cmake -S/construction/science/rdkit/rdkit-Release_2018_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 /usr/bin/make -f External/catch/CMakeFiles/catch.dir/build.make 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/External/catch /construction/science/rdkit/.build 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cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 /usr/bin/make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build [ 96%] Built target SimDivPickers /usr/bin/make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/SimDivPickers /construction/science/rdkit/.build 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/usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 /usr/bin/make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build [ 97%] Built target InfoTheory /usr/bin/make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ML/InfoTheory/Wrap /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/ML/InfoTheory/Wrap 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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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 /usr/bin/make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build [ 99%] Built target ChemicalFeatures /usr/bin/make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend cd /construction/science/rdkit/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/rdkit/rdkit-Release_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_09_3/Code/ChemicalFeatures /construction/science/rdkit/.build /construction/science/rdkit/.build/Code/ChemicalFeatures /construction/science/rdkit/.build/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake /usr/bin/make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build [ 99%] Built target testChemicalFeatures /usr/bin/make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make 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_2018_09_3 /construction/science/rdkit/rdkit-Release_2018_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 /usr/bin/make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build [100%] Built target rdChemicalFeatures /usr/local/bin/cmake -E cmake_progress_start /construction/science/rdkit/.build/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall /usr/bin/make -f External/CoordGen/CMakeFiles/maeparser.dir/build.make External/CoordGen/CMakeFiles/maeparser.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitmaeparser.so cd /construction/science/rdkit/.build/External/CoordGen && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/maeparser.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitmaeparser.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitmaeparser.so.1.2018.09.3 CMakeFiles/maeparser.dir/maeparser/Buffer.cpp.o CMakeFiles/maeparser.dir/maeparser/MaeBlock.cpp.o CMakeFiles/maeparser.dir/maeparser/MaeParser.cpp.o CMakeFiles/maeparser.dir/maeparser/Reader.cpp.o cd /construction/science/rdkit/.build/External/CoordGen && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitmaeparser.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitmaeparser.so.1 CMakeFiles/CMakeRelink.dir/libRDKitmaeparser.so /usr/bin/make -f External/CoordGen/CMakeFiles/coordgenlib.dir/build.make External/CoordGen/CMakeFiles/coordgenlib.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitcoordgenlib.so cd /construction/science/rdkit/.build/External/CoordGen && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/coordgenlib.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitcoordgenlib.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitcoordgenlib.so.1.2018.09.3 CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenFragmentBuilder.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenFragmenter.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenMacrocycleBuilder.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/CoordgenMinimizer.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizer.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerAtom.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerBond.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerFragment.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerMarchingSquares.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerMolecule.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerResidue.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerResidueInteraction.cpp.o CMakeFiles/coordgenlib.dir/coordgenlibs/sketcherMinimizerRing.cpp.o ../../lib/libRDKitmaeparser.so.1.2018.09.3 cd /construction/science/rdkit/.build/External/CoordGen && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitcoordgenlib.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitcoordgenlib.so.1 CMakeFiles/CMakeRelink.dir/libRDKitcoordgenlib.so /usr/bin/make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdCoordGen.so cd /construction/science/rdkit/.build/External/CoordGen/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /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 -std=c++11 -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.1.2018.09.3 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/Dict.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o 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CMakeFiles/rdBase.dir/RDBase.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitDataStructs.so cd /construction/science/rdkit/.build/Code/DataStructs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitDataStructs.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitDataStructs.so.1.2018.09.3 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 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/DataStructs && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitDataStructs.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitDataStructs.so.1 CMakeFiles/CMakeRelink.dir/libRDKitDataStructs.so /usr/bin/make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/cDataStructs.so cd /construction/science/rdkit/.build/Code/DataStructs/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/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,/usr/local/lib ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /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 -std=c++11 -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.1.2018.09.3 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.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/Geometry && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitRDGeometryLib.so.1.2018.09.3 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 -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitAlignment.so cd /construction/science/rdkit/.build/Code/Numerics/Alignment && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitAlignment.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitAlignment.so.1.2018.09.3 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-O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/Numerics/EigenSolvers && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitEigenSolvers.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitEigenSolvers.so.1 CMakeFiles/CMakeRelink.dir/libRDKitEigenSolvers.so /usr/bin/make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitOptimizer.so cd /construction/science/rdkit/.build/Code/Numerics/Optimizer && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitOptimizer.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitOptimizer.so.1.2018.09.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/Numerics/Optimizer && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitOptimizer.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitOptimizer.so.1 CMakeFiles/CMakeRelink.dir/libRDKitOptimizer.so /usr/bin/make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/preinstall Linking CXX shared 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CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/ForceField && /usr/local/bin/cmake -E cmake_symlink_library 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/usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitDistGeometry.so cd /construction/science/rdkit/.build/Code/DistGeom && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitDistGeometry.so.1.2018.09.3 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../lib/libRDKitForceField.so.1.2018.09.3 ../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/DistGeom && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitDistGeometry.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitDistGeometry.so.1 CMakeFiles/CMakeRelink.dir/libRDKitDistGeometry.so /usr/bin/make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/DistGeom.so cd /construction/science/rdkit/.build/Code/DistGeom/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../lib/libRDKitDistGeometry.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitCatalogs.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitCatalogs.so.1.2018.09.3 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/Catalogs && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitCatalogs.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitCatalogs.so.1 CMakeFiles/CMakeRelink.dir/libRDKitCatalogs.so /usr/bin/make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitGraphMol.so cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC 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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 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitGraphMol.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitGraphMol.so.1 CMakeFiles/CMakeRelink.dir/libRDKitGraphMol.so /usr/bin/make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/preinstall Linking CXX shared library 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../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Depictor && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitDepictor.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitDepictor.so.1 CMakeFiles/CMakeRelink.dir/libRDKitDepictor.so /usr/bin/make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdDepictor.so cd /construction/science/rdkit/.build/Code/GraphMol/Depictor/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitSmilesParse.so cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitSmilesParse.so.1.2018.09.3 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 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/SmilesParse && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitSmilesParse.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitSmilesParse.so.1 CMakeFiles/CMakeRelink.dir/libRDKitSmilesParse.so /usr/bin/make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitFileParsers.so cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitFileParsers.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitFileParsers.so.1.2018.09.3 CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.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/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o CMakeFiles/FileParsers.dir/SVGParser.cpp.o ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/FileParsers && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitFileParsers.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitFileParsers.so.1 CMakeFiles/CMakeRelink.dir/libRDKitFileParsers.so /usr/bin/make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make 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cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitSubstructMatch.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitSubstructMatch.so.1 CMakeFiles/CMakeRelink.dir/libRDKitSubstructMatch.so /usr/bin/make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitChemReactions.so cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitChemReactions.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitChemReactions.so.1.2018.09.3 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/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 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-pthread cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitChemReactions.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitChemReactions.so.1 CMakeFiles/CMakeRelink.dir/libRDKitChemReactions.so /usr/bin/make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdChemReactions.so cd /construction/science/rdkit/.build/Code/GraphMol/ChemReactions/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 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CMakeFiles/ChemTransforms.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitChemTransforms.so.1.2018.09.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/ChemTransforms && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitChemTransforms.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitChemTransforms.so.1 CMakeFiles/CMakeRelink.dir/libRDKitChemTransforms.so /usr/bin/make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitSubgraphs.so cd /construction/science/rdkit/.build/Code/GraphMol/Subgraphs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitSubgraphs.so.1.2018.09.3 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Subgraphs && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitSubgraphs.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitSubgraphs.so.1 CMakeFiles/CMakeRelink.dir/libRDKitSubgraphs.so /usr/bin/make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitFilterCatalog.so cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitFilterCatalog.so.1.2018.09.3 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 /usr/local/lib/libboost_serialization.so ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitFilterCatalog.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitFilterCatalog.so.1 CMakeFiles/CMakeRelink.dir/libRDKitFilterCatalog.so /usr/bin/make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdfiltercatalog.so cd /construction/science/rdkit/.build/Code/GraphMol/FilterCatalog/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitFragCatalog.so cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitFragCatalog.so.1.2018.09.3 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 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitFragCatalog.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitFragCatalog.so.1 CMakeFiles/CMakeRelink.dir/libRDKitFragCatalog.so /usr/bin/make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdfragcatalog.so cd /construction/science/rdkit/.build/Code/GraphMol/FragCatalog/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/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,/usr/local/lib ../../../../lib/libRDKitFragCatalog.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/preinstall Linking CXX shared library 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CMakeFiles/Descriptors.dir/USRDescriptor.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 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitDescriptors.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitDescriptors.so.1 CMakeFiles/CMakeRelink.dir/libRDKitDescriptors.so /usr/bin/make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdMolDescriptors.so cd /construction/science/rdkit/.build/Code/GraphMol/Descriptors/Wrap && /usr/local/bin/cmake -E cmake_link_script 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../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitFingerprints.so cd /construction/science/rdkit/.build/Code/GraphMol/Fingerprints && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitFingerprints.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitFingerprints.so.1.2018.09.3 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/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 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--verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitPartialCharges.so cd /construction/science/rdkit/.build/Code/GraphMol/PartialCharges && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitPartialCharges.so.1.2018.09.3 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd 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-Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitMolTransforms.so cd /construction/science/rdkit/.build/Code/GraphMol/MolTransforms && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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/construction/science/rdkit/.build/Code/GraphMol/MolTransforms/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitForceFieldHelpers.so cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitForceFieldHelpers.so.1.2018.09.3 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 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitForceFieldHelpers.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitForceFieldHelpers.so.1 CMakeFiles/CMakeRelink.dir/libRDKitForceFieldHelpers.so /usr/bin/make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdForceFieldHelpers.so cd /construction/science/rdkit/.build/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitDistGeomHelpers.so cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitDistGeomHelpers.so.1.2018.09.3 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/DistGeomHelpers && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitDistGeomHelpers.so.1.2018.09.3 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so 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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 -std=c++11 -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.1.2018.09.3 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o CMakeFiles/MolAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MolAlign && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitMolAlign.so.1.2018.09.3 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 CMakeFiles/rdMolAlign.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MolChemicalFeatures && /usr/local/bin/cmake 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CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitMolChemicalFeatures.so.1.2018.09.3 ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitShapeHelpers.so cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitShapeHelpers.so.1.2018.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/ShapeHelpers && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitShapeHelpers.so.1.2018.09.3 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitShapeHelpers.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitMolCatalog.so cd /construction/science/rdkit/.build/Code/GraphMol/MolCatalog && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitMolCatalog.so.1.2018.09.3 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MolCatalog && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitMolCatalog.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitMolCatalog.so.1 CMakeFiles/CMakeRelink.dir/libRDKitMolCatalog.so /usr/bin/make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdMolCatalog.so cd /construction/science/rdkit/.build/Code/GraphMol/MolCatalog/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitMolCatalog.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitMolDraw2D.so cd /construction/science/rdkit/.build/Code/GraphMol/MolDraw2D && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitMolDraw2D.so.1.2018.09.3 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /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.1.2018.09.3 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 CMakeFiles/rdMolDraw2D.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitMolDraw2D.so.1.2018.09.3 ../../../../lib/libRDKitChemReactions.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitFilterCatalog.so.1.2018.09.3 ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/local/lib/libboost_serialization.so /usr/bin/make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitFMCS.so cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitFMCS.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitFMCS.so.1.2018.09.3 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/FMCS && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitFMCS.so.1.2018.09.3 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitFMCS.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitMolHash.so cd /construction/science/rdkit/.build/Code/GraphMol/MolHash && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolHash.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitMolHash.so.1.2018.09.3 CMakeFiles/MolHash.dir/MolHash.cpp.o CMakeFiles/MolHash.dir/HashToString.cpp.o ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MolHash && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitMolHash.so.1.2018.09.3 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitMolHash.so.1.2018.09.3 ../../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitMMPA.so cd /construction/science/rdkit/.build/Code/GraphMol/MMPA && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMMPA.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitMMPA.so.1.2018.09.3 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MMPA && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitMMPA.so.1.2018.09.3 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitMMPA.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitStructChecker.so cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/StructChecker.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitStructChecker.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitStructChecker.so.1.2018.09.3 CMakeFiles/StructChecker.dir/StructChecker.cpp.o CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o CMakeFiles/StructChecker.dir/StructureFlags.cpp.o CMakeFiles/StructChecker.dir/Utilites.cpp.o CMakeFiles/StructChecker.dir/Pattern.cpp.o CMakeFiles/StructChecker.dir/Stereo.cpp.o CMakeFiles/StructChecker.dir/AtomSymbolMatch.cpp.o CMakeFiles/StructChecker.dir/StripSmallFragments.cpp.o CMakeFiles/StructChecker.dir/ReCharge.cpp.o CMakeFiles/StructChecker.dir/Tautomer.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitStructChecker.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitStructChecker.so.1 CMakeFiles/CMakeRelink.dir/libRDKitStructChecker.so /usr/bin/make -f Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build.make Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdStructChecker.so cd /construction/science/rdkit/.build/Code/GraphMol/StructChecker/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdStructChecker.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdStructChecker.so CMakeFiles/rdStructChecker.dir/structchecker.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitStructChecker.so.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitDescriptors.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitPartialCharges.so.1.2018.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /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 -std=c++11 -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.1.2018.09.3 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/ReducedGraphs && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitReducedGraphs.so.1.2018.09.3 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitReducedGraphs.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /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 -std=c++11 -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.1.2018.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/Trajectory && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitTrajectory.so.1.2018.09.3 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 -std=c++11 -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.1.2018.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o ../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/SubstructLibrary && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitSubstructLibrary.so.1.2018.09.3 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -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.1.2018.09.3 ../../../../lib/libRDKitFingerprints.so.1.2018.09.3 ../../../../lib/libRDKitCatalogs.so.1.2018.09.3 ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /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 -std=c++11 -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.1.2018.09.3 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o ../../../lib/libRDKitFMCS.so.1.2018.09.3 ../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread ../../../lib/libRDKitmaeparser.so.1.2018.09.3 cd /construction/science/rdkit/.build/Code/GraphMol/RGroupDecomposition && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitRGroupDecomposition.so.1.2018.09.3 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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitRGroupDecomposition.so.1.2018.09.3 ../../../../lib/libRDKitFMCS.so.1.2018.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitFileParsers.so.1.2018.09.3 ../../../../lib/libRDKitDepictor.so.1.2018.09.3 ../../../../lib/libRDKitMolAlign.so.1.2018.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /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 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitMolInterchange.so.1.2018.09.3 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/MolInterchange && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitMolInterchange.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitMolInterchange.so.1 CMakeFiles/CMakeRelink.dir/libRDKitMolInterchange.so /usr/bin/make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdMolInterchange.so cd /construction/science/rdkit/.build/Code/GraphMol/MolInterchange/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -Wl,-z,origin,-rpath,/usr/local/lib ../../../../lib/libRDKitMolInterchange.so.1.2018.09.3 ../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitSLNParse.so cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitSLNParse.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitSLNParse.so.1.2018.09.3 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 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/GraphMol/SLNParse && /usr/local/bin/cmake -E cmake_symlink_library 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../../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../../lib/libRDKitRDBoost.so.1.2018.09.3 /usr/local/lib/libpython3.6m.so /usr/local/lib/libboost_python36.so /usr/local/lib/libboost_serialization.so ../../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdmolops.so cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o 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../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitSubgraphs.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitMolTransforms.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/local/lib/libboost_serialization.so /usr/bin/make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdqueries.so cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 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../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/bin/make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/rdtrajectory.so cd /construction/science/rdkit/.build/Code/GraphMol/Wrap && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o 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../../../lib/libRDKitEigenSolvers.so.1.2018.09.3 ../../../lib/libRDKitAlignment.so.1.2018.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.3 ../../../lib/libRDKitForceField.so.1.2018.09.3 ../../../lib/libRDKitOptimizer.so.1.2018.09.3 ../../../lib/libRDKitTrajectory.so.1.2018.09.3 ../../../lib/libRDKitcoordgenlib.so.1.2018.09.3 ../../../lib/libRDKitSmilesParse.so.1.2018.09.3 ../../../lib/libRDKitmaeparser.so.1.2018.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.3 ../../../lib/libRDKitGraphMol.so.1.2018.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.3 ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread /usr/local/lib/libboost_serialization.so cd /construction/science/rdkit/.build/Code/GraphMol/MolStandardize && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitMolStandardize.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitMolStandardize.so.1 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cmake_link_script CMakeFiles/SimDivPickers.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitSimDivPickers.so.1.2018.09.3 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2018.09.3 ../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/SimDivPickers && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitSimDivPickers.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitSimDivPickers.so.1 CMakeFiles/CMakeRelink.dir/libRDKitSimDivPickers.so /usr/bin/make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make 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Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libRDKitInfoTheory.so cd /construction/science/rdkit/.build/Code/ML/InfoTheory && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -mpopcnt -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o CMakeFiles/CMakeRelink.dir/libRDKitInfoTheory.so.1.2018.09.3 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2018.09.3 ../../../lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread cd /construction/science/rdkit/.build/Code/ML/InfoTheory && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libRDKitInfoTheory.so.1.2018.09.3 CMakeFiles/CMakeRelink.dir/libRDKitInfoTheory.so.1 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-------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for rdkit-2018.09.3_2 file sizes/checksums [1498]: .......... done packing files [1498]: .......... done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 26 JUL 2019 at 09:23:38 UTC Duration: 00:45:49