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Maintainer: [email protected] Log URL: http://beefy15.nyi.freebsd.org/data/130i386-default/814fc6db724a/logs/rdkit-2021.09.4.log Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=130i386-default&build=814fc6db724a Log: =>> Building science/rdkit build started at Sat Jan 22 08:14:51 UTC 2022 port directory: /usr/ports/science/rdkit package name: rdkit-2021.09.4 building for: FreeBSD 130i386-default-job-04 13.0-RELEASE-p6 FreeBSD 13.0-RELEASE-p6 i386 maintained by: [email protected] Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400008 Jail OSVERSION: 1300139 Job Id: 04 ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1300139 UNAME_v=FreeBSD 13.0-RELEASE-p6 UNAME_r=13.0-RELEASE-p6 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-21-g883afb07 MASTERMNT=/usr/local/poudriere/data/.m/130i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/130i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=130i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/130i386-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for rdkit-2021.09.4: DOCS=on: Build and/or install documentation PGSQL=off: Build the PostgreSQL cartridge PYTHON=on: Python bindings or support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.8" XDG_DATA_HOME=/wrkdirs/usr/ports/science/rdkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/rdkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/rdkit/work/.cache HOME=/wrkdirs/usr/ports/science/rdkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/rdkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/science/rdkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/rdkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/rdkit/work/.cache HOME=/wrkdirs/usr/ports/science/rdkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/rdkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/science/rdkit/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -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" --End MAKE_ENV-- --PLIST_SUB-- SHLIB_VER=2021.09.4 PORTDOCS="" DOCS="" NO_DOCS="@comment " PGSQL="@comment " NO_PGSQL="" PYTHON="" NO_PYTHON="@comment " LITTLE_ENDIAN="" CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.8 PYTHON_LIBDIR=lib/python3.8 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.8/site-packages PYTHON_SUFFIX=38 PYTHON_EXT_SUFFIX=.cpython-38 PYTHON_VER=3.8 PYTHON_VERSION=python3.8 PYTHON2="@comment " PYTHON3="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/RDKit" EXAMPLESDIR="share/examples/rdkit" DATADIR="share/RDKit" WWWDIR="www/rdkit" ETCDIR="etc/rdkit" --End PLIST_SUB-- --SUB_LIST-- DOCS="" NO_DOCS="@comment " PGSQL="@comment " NO_PGSQL="" 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 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. 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[130i386-default-job-04] Extracting pkg-1.17.5_1: .......... done ===> rdkit-2021.09.4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of rdkit-2021.09.4 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by rdkit-2021.09.4 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by rdkit-2021.09.4 for building => SHA256 Checksum OK for rdkit-2021.09.4/Comic_Neue.zip. => SHA256 Checksum OK for rdkit-2021.09.4/rdkit-rdkit-Release_2021_09_4_GH0.tar.gz. => SHA256 Checksum OK for rdkit-2021.09.4/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by rdkit-2021.09.4 for building ===> Extracting for rdkit-2021.09.4 => SHA256 Checksum OK for rdkit-2021.09.4/Comic_Neue.zip. => SHA256 Checksum OK for rdkit-2021.09.4/rdkit-rdkit-Release_2021_09_4_GH0.tar.gz. => SHA256 Checksum OK for rdkit-2021.09.4/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz. Archive: /portdistfiles/rdkit-2021.09.4/Comic_Neue.zip extracting: OFL.txt extracting: ComicNeue-Light.ttf extracting: ComicNeue-LightItalic.ttf extracting: ComicNeue-Regular.ttf extracting: ComicNeue-Italic.ttf extracting: ComicNeue-Bold.ttf extracting: ComicNeue-BoldItalic.ttf =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ <snip> In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/MACCS.cpp:13: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/RDKitBase.h:25: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18: In file included from /usr/local/include/boost/random.hpp:36: In file included from /usr/local/include/boost/random/additive_combine.hpp:27: /usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if(_x <= 0 && _x != 0) { ~~~~~~~~^~~~~~~~~~ /usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [ 49% 297/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function - fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/MHFP.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/MHFP.cpp:26: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/MolOps.h:23: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/SanitException.h:16: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/GraphMol.h:19: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/ROMol.h:37: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18: In file included from /usr/local/include/boost/random.hpp:36: In file included from /usr/local/include/boost/random/additive_combine.hpp:27: /usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if(_x <= 0 && _x != 0) { ~~~~~~~~^~~~~~~~~~ /usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [ 49% 298/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function - fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:18: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/AtomPairGenerator.h:16: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/FingerprintUtil.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/RDKitBase.h:25: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18: In file included from /usr/local/include/boost/random.hpp:36: In file included from /usr/local/include/boost/random/additive_combine.hpp:27: /usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if(_x <= 0 && _x != 0) { ~~~~~~~~^~~~~~~~~~ /usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [ 50% 299/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function - fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:11: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/RDKitBase.h:25: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18: In file included from /usr/local/include/boost/random.hpp:36: In file included from /usr/local/include/boost/random/additive_combine.hpp:27: /usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if(_x <= 0 && _x != 0) { ~~~~~~~~^~~~~~~~~~ /usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [ 50% 300/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function - fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/MorganGenerator.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/MorganGenerator.cpp:11: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/RDKitBase.h:25: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18: In file included from /usr/local/include/boost/random.hpp:36: In file included from /usr/local/include/boost/random/additive_combine.hpp:27: /usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if(_x <= 0 && _x != 0) { ~~~~~~~~^~~~~~~~~~ /usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [ 50% 301/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function - fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:12: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/RDKitBase.h:25: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18: In file included from /usr/local/include/boost/random.hpp:36: In file included from /usr/local/include/boost/random/additive_combine.hpp:27: /usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if(_x <= 0 && _x != 0) { ~~~~~~~~^~~~~~~~~~ /usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. 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[ 50% 303/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function - fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:11: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:16: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/FingerprintUtil.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/RDKitBase.h:25: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18: In file included from /usr/local/include/boost/random.hpp:36: In file included from /usr/local/include/boost/random/additive_combine.hpp:27: /usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if(_x <= 0 && _x != 0) { ~~~~~~~~^~~~~~~~~~ /usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [ 50% 304/598] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -shared -Wl,-soname,libRDKitFingerprints.so.1 -o lib/libRDKitFingerprints.so.1.2021.09.4 Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o Code/ 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-I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno- format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:212:23: error: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list [-Wc++11-narrowing] npy_intp size[1] = {ebv->size()}; ^~~~~~~~~~~ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:212:23: note: insert an explicit cast to silence this issue npy_intp size[1] = {ebv->size()}; ^~~~~~~~~~~ static_cast<npy_intp>( ) /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:237:23: error: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list [-Wc++11-narrowing] npy_intp size[1] = {fp->size()}; ^~~~~~~~~~ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:237:23: note: insert an explicit cast to silence this issue npy_intp size[1] = {fp->size()}; ^~~~~~~~~~ static_cast<npy_intp>( ) /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:237:23: error: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list [-Wc++11-narrowing] npy_intp size[1] = {fp->size()}; ^~~~~~~~~~ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:479:12: note: in instantiation of function template specialization 'RDKit::FingerprintWrapper::getNumPyCountFingerprint<unsigned int>' requested here getNumPyCountFingerprint<std::uint32_t>, ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:237:23: note: insert an explicit cast to silence this issue npy_intp size[1] = {fp->size()}; ^~~~~~~~~~ static_cast<npy_intp>( ) /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:212:23: error: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list [-Wc++11-narrowing] npy_intp size[1] = {ebv->size()}; ^~~~~~~~~~~ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:526:37: note: in instantiation of function template specialization 'RDKit::FingerprintWrapper::getNumPyFingerprint<unsigned int>' requested here .def("GetFingerprintAsNumPy", getNumPyFingerprint<std::uint32_t>, ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:212:23: note: insert an explicit cast to silence this issue npy_intp size[1] = {ebv->size()}; ^~~~~~~~~~~ static_cast<npy_intp>( ) /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:237:23: error: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list [-Wc++11-narrowing] npy_intp size[1] = {fp->size()}; ^~~~~~~~~~ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:630:12: note: in instantiation of function template specialization 'RDKit::FingerprintWrapper::getNumPyCountFingerprint<unsigned long long>' requested here getNumPyCountFingerprint<std::uint64_t>, ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:237:23: note: insert an explicit cast to silence this issue npy_intp size[1] = {fp->size()}; ^~~~~~~~~~ static_cast<npy_intp>( ) /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:212:23: error: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list [-Wc++11-narrowing] npy_intp size[1] = {ebv->size()}; ^~~~~~~~~~~ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:677:37: note: in instantiation of function template specialization 'RDKit::FingerprintWrapper::getNumPyFingerprint<unsigned long long>' requested here .def("GetFingerprintAsNumPy", getNumPyFingerprint<std::uint64_t>, ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:212:23: note: insert an explicit cast to silence this issue npy_intp size[1] = {ebv->size()}; ^~~~~~~~~~~ static_cast<npy_intp>( ) 6 errors generated. ninja: build stopped: subcommand failed. *** Error code 1 Stop. make: stopped in /usr/ports/science/rdkit
