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Maintainer: [email protected] Last committer: [email protected] Ident: $FreeBSD: head/science/rdkit/Makefile 529063 2020-03-24 19:54:57Z antoine $ Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p545731_s364466/logs/rdkit-2018.09.3_6.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p545731_s364466 Log: =>> Building science/rdkit build started at Sun Aug 23 17:21:18 UTC 2020 port directory: /usr/ports/science/rdkit package name: rdkit-2018.09.3_6 building for: FreeBSD head-amd64-default-job-02 13.0-CURRENT FreeBSD 13.0-CURRENT 1300110 amd64 maintained by: [email protected] Makefile ident: $FreeBSD: head/science/rdkit/Makefile 529063 2020-03-24 19:54:57Z antoine $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300100 Jail OSVERSION: 1300110 Job Id: 02 !!! Jail is newer than host. (Jail: 1300110, Host: 1300100) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300110 UNAME_v=FreeBSD 13.0-CURRENT 1300110 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root 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=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-amd64-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-2018.09.3_6: DOCS=on: Build and/or install documentation 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/python3.7" XDG_DATA_HOME=/wrkdirs/usr/ports/science/rdkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/rdkit/work 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-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/rdkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/rdkit/work 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=2018.09.3 PORTDOCS="" DOCS="" NO_DOCS="@comment " PYTHON="" NO_PYTHON="@comment " LITTLE_ENDIAN="" CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_VER=3.7 PYTHON_VERSION=python3.7 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 " 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 #### /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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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 11.0.0 ([email protected]:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.0 ([email protected]:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: x86_64-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" "-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 11.0.0 ([email protected]:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300110 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 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-- =======================<phase: check-sanity >============================ ===> License BSD3CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> rdkit-2018.09.3_6 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.14.7.txz [head-amd64-default-job-02] Installing pkg-1.14.7... [head-amd64-default-job-02] Extracting pkg-1.14.7: .......... done ===> rdkit-2018.09.3_6 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of rdkit-2018.09.3_6 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by rdkit-2018.09.3_6 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by rdkit-2018.09.3_6 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_6 for building ===> Extracting for rdkit-2018.09.3_6 => 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_6 ===> Applying FreeBSD patches for rdkit-2018.09.3_6 from /usr/ports/science/rdkit/files =========================================================================== =======================<phase: build-depends >============================ ===> rdkit-2018.09.3_6 depends on package: catch>0 - not found ===> Installing existing package /packages/All/catch-2.13.0.txz <snip> 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, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [439/708] /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/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 -pthread -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o Code/GraphMol/ReducedGraphs/C MakeFiles/testReducedGraphs.dir/test1.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/ReducedGraphs/test1.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/ReducedGraphs/test1.cpp:13: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/RDKitBase.h:25: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/Conformer.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/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, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [440/708] /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/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 -MD -MT Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/structchecker.cpp.o -MF Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/structchecker.cpp.o.d -o Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/structchecker.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/Wrap/structchecker.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/Wrap/structchecker.cpp:35: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/StructChecker.h:27: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/RDKitBase.h:25: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/StructChecker/../Conformer.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/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, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [441/708] /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/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -MF Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cp p.o.d -o Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp:11: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/RDKitBase.h:25: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/Conformer.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/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, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [442/708] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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,libRDKitReducedGraphs.so.1 -o lib/libRDKitReducedGraphs.so.1.2018.09.3 Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.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 && : [443/708] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitReducedGraphs.so.1.2018.09.3 lib/libRDKitReducedGraphs.so.1 lib/libRDKitReducedGraphs.so && : [444/708] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o Code/GraphMol/ReducedGraphs/testReducedGraphs -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.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 && : [445/708] /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/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 -MD -MT Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -MF Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o.d -o Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/RDBoost/boost_numpy.h:8: In file included from /usr/local/include/boost/python/numpy.hpp:11: /usr/local/include/boost/python/numpy/ndarray.hpp:179:114: warning: unused parameter 'enabled' [-Wunused-parameter] typename boost::enable_if< boost::python::detail::is_integral<typename Container::value_type> >::type * enabled = NULL) ^ In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp:17: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/GraphMol.h:19: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/ROMol.h:36: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/Conformer.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/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, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 2 warnings generated. [446/708] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 -o rdkit/Chem/rdReducedGraphs.so Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.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/libpython3.7m.so /usr/local/lib/libboost_python37.so /usr/local/lib/libboost_serialization.so lib/libRDKitDataStructs.so.1.2018.09.3 lib/libRDKitRDGeneral.so.1.2018.09.3 -pthread && : [447/708] /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/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 -pthread -MD -MT Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o Code/GraphMol/Trajectory/C MakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/Trajectory/trajectoryTest.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/Trajectory/trajectoryTest.cpp:13: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/Trajectory/Trajectory.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/Trajectory/Snapshot.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/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, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [448/708] /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/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o Code/GraphMol/T rajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/Trajectory/Trajectory.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/Trajectory/Trajectory.cpp:13: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/ROMol.h:36: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/Conformer.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/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, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 1 warning generated. [449/708] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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,libRDKitTrajectory.so.1 -o lib/libRDKitTrajectory.so.1.2018.09.3 Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.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 && : [450/708] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitTrajectory.so.1.2018.09.3 lib/libRDKitTrajectory.so.1 lib/libRDKitTrajectory.so && : [451/708] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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,libRDKitOptimizer.so.1 -o lib/libRDKitOptimizer.so.1.2018.09.3 Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.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 && : [452/708] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitOptimizer.so.1.2018.09.3 lib/libRDKitOptimizer.so.1 lib/libRDKitOptimizer.so && : [453/708] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe 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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 && : [474/708] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o Code/ForceField/UFF/testUFFForceField -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.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/lib RDKitRDGeometryLib.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 && : [475/708] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o Code/ForceField/MMFF/testMMFFForceField -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.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.1.201 8.09.3 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 && : [476/708] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o Code/GraphMol/resMolSupplierTest -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.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/libRDKitRDGe ometryLib.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 && : [477/708] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o Code/GraphMol/graphmoltestPicklerGlobalSetting -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.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/libRDKitGraphM ol.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 && : [478/708] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o Code/GraphMol/molBundleTest -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.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 && : [479/708] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o Code/GraphMol/graphmoltestPickler -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.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/libRDKitRDGeometr yLib.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 && : [480/708] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o Code/GraphMol/hanoiTest -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.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 l ib/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 && : FAILED: Code/GraphMol/hanoiTest : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o Code/GraphMol/hanoiTest -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.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/libRDKi tDataStructs.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 && : ld: error: undefined symbol: std::__1::__rs_get() >>> referenced by hanoitest.cpp >>> Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o:(void >>> std::__1::random_shuffle<std::__1::__wrap_iter<unsigned int*> >>> >(std::__1::__wrap_iter<unsigned int*>, std::__1::__wrap_iter<unsigned >>> int*>)) ld: error: undefined symbol: std::__1::__rs_default::~__rs_default() >>> referenced by hanoitest.cpp >>> Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o:(void >>> std::__1::random_shuffle<std::__1::__wrap_iter<unsigned int*> >>> >(std::__1::__wrap_iter<unsigned int*>, std::__1::__wrap_iter<unsigned >>> int*>)) >>> referenced by hanoitest.cpp >>> Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o:(void >>> std::__1::random_shuffle<std::__1::__wrap_iter<unsigned int*> >>> >(std::__1::__wrap_iter<unsigned int*>, std::__1::__wrap_iter<unsigned >>> int*>)) ld: error: undefined symbol: std::__1::__rs_default::operator()() >>> referenced by hanoitest.cpp >>> Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o:(long >>> std::__1::uniform_int_distribution<long>::operator()<std::__1::__rs_default>(std::__1::__rs_default&, >>> std::__1::uniform_int_distribution<long>::param_type const&)) >>> referenced by hanoitest.cpp >>> Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o:(long >>> std::__1::uniform_int_distribution<long>::operator()<std::__1::__rs_default>(std::__1::__rs_default&, >>> std::__1::uniform_int_distribution<long>::param_type const&)) >>> referenced by hanoitest.cpp >>> Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o:(long >>> std::__1::uniform_int_distribution<long>::operator()<std::__1::__rs_default>(std::__1::__rs_default&, >>> std::__1::uniform_int_distribution<long>::param_type const&)) >>> referenced 1 more times c++: error: linker command failed with exit code 1 (use -v to see invocation) [481/708] /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/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/External -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -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 -pthread -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTe st.cpp.o -MF Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp:19: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/SubstructLibrary.h:39: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/Fingerprints/Fingerprints.h:16: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/DataStructs/SparseIntVect.h:20: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/RDGeneral/StreamOps.h:22: In file included from /usr/local/include/boost/detail/endian.hpp:9: /usr/local/include/boost/predef/detail/endian_compat.h:11:9: warning: The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include <boost/predef/other/endian.h> and use BOOST_ENDIAN_*_BYTE instead [-W#pragma-messages] #pragma message("The use of BOOST_*_ENDIAN and BOOST_BYTE_ORDER is deprecated. Please include <boost/predef/other/endian.h> and use BOOST_ENDIAN_*_BYTE instead") ^ In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp:17: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/RDKitBase.h:25: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/GraphMol/Conformer.h:14: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Geometry/point.h:24: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/Code/Numerics/Vector.h:15: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2018_09_3/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, 25214903917, 11, 281474976710656>::seed' requested here { lcf.seed(cnv(x0)); } ^ 2 warnings generated. ninja: build stopped: subcommand failed. ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/science/rdkit _______________________________________________ [email protected] mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "[email protected]"
