From nobody Sat Jan 22 08:38:51 2022 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id B99E819797A3 for ; Sat, 22 Jan 2022 08:38:51 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4JgqQz3KcWz3CN0; Sat, 22 Jan 2022 08:38:51 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy15.nyi.freebsd.org (beefy15.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:1e]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 515043DDC; Sat, 22 Jan 2022 08:38:51 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy15.nyi.freebsd.org (localhost [127.0.0.1]) by beefy15.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 20M8cpGJ046947; Sat, 22 Jan 2022 08:38:51 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy15.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 20M8cp7F046946; Sat, 22 Jan 2022 08:38:51 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 22 Jan 2022 08:38:51 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202201220838.20M8cp7F046946@beefy15.nyi.freebsd.org> To: yuri@FreeBSD.org Subject: [package - 130i386-default][science/rdkit] Failed for rdkit-2021.09.4 in build Cc: pkg-fallout@FreeBSD.org ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1642840731; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=/L1fHpK+FwcWzMdgNLI6duojqg/PlWhIVtTvvgtT10E=; b=hf6K5abN7Kk4C8t+K8KUYnjVTKQnompc5/OPD37tHigcLpAVUiwjwL4+r3zJvUXSOhbU3O XRsZpupkmh+XcxB+tDwspiuPKIrnRWNRVomfd3dn3gs/599fu2OLBi3Fv2cKz0q9C++6VR hw9gfUdAImXNI93/EBNQMgj1RbjAqT8uasWw5l7TkMfgMpwgEQGcuG4x3gLJ8PvaLBlTcP mtpPS3jgux45nmp2bRORyJN4U13WrNlpO8BICQ5tja+c2kXfmmYIreD4B7JQ8O8ch16Wuc rGVEiAhRuFOIyPGX6atP3kdmGNxd89ScYcMTDXe5Zj8MDOLx/0juhl8qQi4wCQ== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1642840731; a=rsa-sha256; cv=none; b=NFMtxCM6BoYfwGVUD6nXlGGYdlKLCygSo7dddpouEwoTRA82SFRZc80ukh4pppfOrWA/5H Wb30pFpoHN2amWf2jzh85jaQLqj6ByrpFq7I2CRyuRELD82r+mEfFrfTEiG4oU/Qbs5FDt 6ULxZlhxxtlVMccp+9vQBnlIuMAFfTEtmmeaP9LE3mFrUEUzm+58OQGAoVAyMmzPn1tmIm QNXrafySf3bhsjhCNVd1zg7tGF9RZDk5n4xppNMJROajob80NLNq5UKGyv3Tvw8GTACSVX Z7h1NIdmd2bflhejLBiOHO9VwzmaDKQhK23Bu5+tUaEcCjHOqnCDVRgnfyGd+Q== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org 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: yuri@FreeBSD.org 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-- yuri@FreeBSD.org --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. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-m" "elf_i386_fbsd" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=13.0-RELEASE-p6 OSREL=13.0 OSVERSION=1300139 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 524288 stack size (kbytes, -s) 65536 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===> License BSD3CLAUSE accepted by the user =========================================================================== =================================================== ===> rdkit-2021.09.4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.5_1.pkg [130i386-default-job-04] Installing pkg-1.17.5_1... [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 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by rdkit-2021.09.4 for building =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> 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 =========================================================================== =================================================== =========================================================================== =================================================== 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::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::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::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::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::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::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [ 50% 302/598] /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/FingerprintUtil.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/FingerprintUtil.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/FingerprintUtil.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::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [ 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::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/ GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.build/lib: lib/libRDKitSubgraphs.so.1.2021.09.4 lib/libRDKitSubstructMatch.so.1.2021.09.4 lib/libRDKitSmilesParse.so.1.2021.09.4 lib/libRDKitGraphMol.so.1.2021.09.4 lib/libRDKitRDGeometryLib.so.1.2021.09.4 lib/libRDKitDataStructs.so.1.2021.09.4 lib/libRDKitRingDecomposerLib.so.1.2021.09.4 lib/libRDKitRDGeneral.so.1.2021.09.4 -pthread -ldl && : [ 51% 305/598] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitFingerprints.so.1.2021.09.4 lib/libRDKitFingerprints.so.1 lib/libRDKitFingerprints.so && : [ 51% 306/598] : && /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 -pthread -shared -L/usr/local/lib -fstack-protector-strong -shared -o rdkit/Chem/rdMHFPFingerprint.so Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.build/lib:/usr/local/lib: lib/libRDKitFingerprints.so.1.2021.09.4 lib/libRDKitRDBoost.so.1.2021.09.4 lib/libRDKitSubgraphs.so.1.2021.09.4 lib/libRDKitSubstructMatch.so.1.2021.09.4 lib/libRDKitSmilesParse.so.1.2021.09.4 lib/libRDKitGraphMol.so.1.2021.09.4 lib/libRDKitRDGeometryLib.so.1.2021.09.4 lib/libRDKitDataStructs.so.1.2021.09.4 lib/libRDKitRingDecomposerLib.so.1.2021.09.4 /usr/local/lib/libpython3.8.so /usr/local/lib/libboost_python38. so lib/libRDKitRDGeneral.so.1.2021.09.4 -pthread -ldl && : [ 51% 307/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -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 -DrdFingerprintGenerator_EXPORTS -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 FAILED: Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -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 -DrdFingerprintGenerator_EXPORTS -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( ) /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( ) /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' requested here getNumPyCountFingerprint, ^ /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( ) /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' requested here .def("GetFingerprintAsNumPy", getNumPyFingerprint, ^ /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( ) /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' requested here getNumPyCountFingerprint, ^ /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( ) /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' requested here .def("GetFingerprintAsNumPy", getNumPyFingerprint, ^ /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( ) 6 errors generated. ninja: build stopped: subcommand failed. *** Error code 1 Stop. make: stopped in /usr/ports/science/rdkit