[package - main-arm64-default][science/rdkit] Failed for rdkit-2023.09.3 in build
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Date: Fri, 15 Dec 2023 20:13:45 UTC
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: https://pkg-status.freebsd.org/ampere2/data/main-arm64-default/p1dd4264fe4a8_s59dba901f2/logs/rdkit-2023.09.3.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p1dd4264fe4a8_s59dba901f2
Log:
=>> Building science/rdkit
build started at Fri Dec 15 20:04:28 UTC 2023
port directory: /usr/ports/science/rdkit
package name: rdkit-2023.09.3
building for: FreeBSD main-arm64-default-job-13 15.0-CURRENT FreeBSD 15.0-CURRENT 1500007 arm64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 2544 Dec 14 01:05 /usr/ports/science/rdkit/Makefile
Ports top last git commit: 1dd4264fe4a
Ports top unclean checkout: no
Port dir last git commit: 994b9154c9e
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.0
Host OSVERSION: 1500006
Jail OSVERSION: 1500007
Job Id: 13
!!! Jail is newer than host. (Jail: 1500007, Host: 1500006) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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===> The following configuration options are available for rdkit-2023.09.3:
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/python3.9" 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 PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/rdkit/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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--End MAKE_ENV--
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SHLIB_VER=2023.09.3 PORTDOCS="" DOCS="" NO_DOCS="@comment " PGSQL="@comment " NO_PGSQL="" PYTHON="" NO_PYTHON="@comment " LITTLE_ENDIAN="" CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=15.0 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 " PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" 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
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#### ####
# 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.
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GID=0
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--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> rdkit-2023.09.3 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.9.pkg
[main-arm64-default-job-13] Installing pkg-1.20.9...
[main-arm64-default-job-13] Extracting pkg-1.20.9: .......... done
===> rdkit-2023.09.3 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of rdkit-2023.09.3
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE accepted by the user
=> Comic_Neue.zip doesn't seem to exist in /portdistfiles/rdkit-2023.09.3.
=> Attempting to fetch https://fonts.google.com/download?family=Comic%20Neue&dummy=/Comic_Neue.zip
fetch: https://fonts.google.com/download?family=Comic%20Neue&dummy=/Comic_Neue.zip: size unknown
fetch: https://fonts.google.com/download?family=Comic%20Neue&dummy=/Comic_Neue.zip: size of remote file is not known
Comic_Neue.zip 176 kB 2554 kBps 00s
=> rdkit-rdkit-Release_2023_09_3_GH0.tar.gz doesn't seem to exist in /portdistfiles/rdkit-2023.09.3.
=> Attempting to fetch https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2023_09_3?dummy=/rdkit-rdkit-Release_2023_09_3_GH0.tar.gz
fetch: https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2023_09_3?dummy=/rdkit-rdkit-Release_2023_09_3_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2023_09_3?dummy=/rdkit-rdkit-Release_2023_09_3_GH0.tar.gz: size of remote file is not known
rdkit-rdkit-Release_2023_09_3_GH0.tar.gz 76 MB 9 MBps 07s
=> rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz doesn't seem to exist in /portdistfiles/rdkit-2023.09.3.
=> Attempting to fetch https://codeload.github.com/rareylab/RingDecomposerLib/tar.gz/v1.1.3_rdkit?dummy=/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz
fetch: https://codeload.github.com/rareylab/RingDecomposerLib/tar.gz/v1.1.3_rdkit?dummy=/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/rareylab/RingDecomposerLib/tar.gz/v1.1.3_rdkit?dummy=/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz: size of remote file is not known
rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz 134 kB 5451 kBps 00s
===> Fetching all distfiles required by rdkit-2023.09.3 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by rdkit-2023.09.3 for building
=> SHA256 Checksum OK for rdkit-2023.09.3/Comic_Neue.zip.
=> SHA256 Checksum OK for rdkit-2023.09.3/rdkit-rdkit-Release_2023_09_3_GH0.tar.gz.
=> SHA256 Checksum OK for rdkit-2023.09.3/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by rdkit-2023.09.3 for building
===> Extracting for rdkit-2023.09.3
=> SHA256 Checksum OK for rdkit-2023.09.3/Comic_Neue.zip.
=> SHA256 Checksum OK for rdkit-2023.09.3/rdkit-rdkit-Release_2023_09_3_GH0.tar.gz.
=> SHA256 Checksum OK for rdkit-2023.09.3/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz.
Archive: /portdistfiles/rdkit-2023.09.3/Comic_Neue.zip
extracting: OFL.txt
extracting: ComicNeue-Light.ttf
<snip>
-- Found maeparser: /usr/local/include
-- coordgen include dir set as /usr/local/include
-- coordgen libraries set as '/usr/local/lib/libcoordgen.so'
-- Found coordgen: /usr/local/include
-- Found RingDecomposerLib source in /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib
CMake Warning (dev) at Code/GraphMol/FilterCatalog/CMakeLists.txt:5 (find_package):
Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
are removed. Run "cmake --help-policy CMP0148" for policy details. Use
the cmake_policy command to set the policy and suppress this warning.
This warning is for project developers. Use -Wno-dev to suppress it.
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Data/Fonts/ComicNeue-Regular.ttf already there, skipping the download
-- Found Freetype: /usr/local/lib/libfreetype.so (found version "2.13.2")
-- Found Boost: /usr/local/include (found suitable version "1.83.0", minimum required is "1.58.0") found components: program_options
-- Found RapidJSON source in /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External
-- Configuring done (5.0s)
-- Generating done (1.2s)
CMake Warning:
Manually-specified variables were not used by the project:
CATCH_DIR
CMAKE_COLOR_MAKEFILE
CMAKE_VERBOSE_MAKEFILE
Python3_EXECUTABLE
Python_EXECUTABLE
RDK_OPTIMIZE_NATIVE
-- Build files have been written to: /wrkdirs/usr/ports/science/rdkit/work/.build
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for rdkit-2023.09.3
[ 0% 3/640] cd /wrkdirs/usr/ports/science/rdkit/work/.build/External/INCHI-API && /usr/local/bin/cmake -E copy /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/INCHI-API/python/noinchi.py /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/rdkit/Chem/inchi.py
[ 0% 4/640] /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DRingDecomposerLib_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-array-bounds -fPIC -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -O2 -pipe -fstack-protector-str
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[ 0% 5/640] /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DRingDecomposerLib_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-array-bounds -fPIC -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -O2 -pipe -fstack-protector-str
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[ 0% 6/640] /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DRingDecomposerLib_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-array-bounds -fPIC -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -O2 -pipe -fstack-protector-str
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[ 0% 7/640] /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DRingDecomposerLib_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-array-bounds -fPIC -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -O2 -pipe -fstack-protector-str
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[ 5% 35/640] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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 -DNDEBUG -fstack-protector-strong -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o lib/libRDKitRDGeneral.so.1.2023.09.3 Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -Wl,-rpath,/usr/local/lib: -ldl -lpthread /usr/local/lib/libboost_system.so /usr/local/lib/libboost_serialization.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/l
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[ 5% 36/640] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitRDGeneral.so.1.2023.09.3 lib/libRDKitRDGeneral.so.1 lib/libRDKitRDGeneral.so && :
[ 5% 37/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DRDStreams_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical
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[ 5% 38/640] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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 -DNDEBUG -fstack-protector-strong -shared -Wl,-soname,libRDKitRDStreams.so.1 -o lib/libRDKitRDStreams.so.1.2023.09.3 Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -Wl,-rpath,/usr/local/lib: -lpthread /usr/local/lib/libboost_system.so /usr/local/lib/libboost_serialization.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_serialization.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so && :
[ 5% 39/640] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitRDStreams.so.1.2023.09.3 lib/libRDKitRDStreams.so.1 lib/libRDKitRDStreams.so && :
[ 5% 40/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logi
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[ 6% 42/640] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitRDBoost.so.1.2023.09.3 lib/libRDKitRDBoost.so.1 lib/libRDKitRDBoost.so && :
[ 6% 43/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasin
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[ 6% 44/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasin
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[ 6% 45/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasin
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[ 6% 46/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasin
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[ 7% 47/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasin
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[ 7% 48/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasin
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[ 7% 49/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasin
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[ 9% 65/640] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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 -DNDEBUG -fstack-protector-strong -pthread -shared -L/usr/local/lib -fstack-protector-strong -shared -o rdkit/DataStructs/cDataStructs.so Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -Wl,-rpath,/wrkdirs/us
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[ 10% 66/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno
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[ 10% 67/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno
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[ 10% 68/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno
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[ 10% 69/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno
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[ 10% 70/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno
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[ 10% 71/640] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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 -DNDEBUG -fstack-protector-strong -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o lib/libRDKitRDGeometryLib.so.1.2023.09.3 Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.build/lib:/usr/local/lib: lib/libRDKitDataStructs.so.1.2023.09.3 lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/local/lib/libboost_system.so /usr/local/lib/libboost_serialization.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost
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[ 10% 72/640] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitRDGeometryLib.so.1.2023.09.3 lib/libRDKitRDGeometryLib.so.1 lib/libRDKitRDGeometryLib.so && :
[ 11% 73/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdGeometry_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses
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[ 11% 74/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdGeometry_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses
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[ 11% 75/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdGeometry_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses
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[ 11% 76/640] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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 -DNDEBUG -fstack-protector-strong -pthread -shared -L/usr/local/lib -fstack-protector-strong -shared -o rdkit/Geometry/rdGeometry.so Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.build/lib:/usr/local/lib: lib/libRDKitRDGeometryLib.so.1.2023.09.3 lib/libRDKitRDBoost.so.1.2023.09.3 lib/libRDKitDataStructs.so.1.2023.09.3 /usr/local/lib/libpython3.9.so /usr/local/lib/libboost_python39.so lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/local/lib/libboost_system.so /usr/local/lib/libboost_serialization.so /usr/local/lib/lib
boost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_serialization.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so -lpthread -ldl && :
[ 11% 77/640] /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical
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[ 11% 78/640] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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 -DNDEBUG -fstack-protector-strong -shared -Wl,-soname,libRDKitAlignment.so.1 -o lib/libRDKitAlignment.so.1.2023.09.3 Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.build/lib:/usr/local/lib: lib/libRDKitRDGeometryLib.so.1.2023.09.3 lib/libRDKitDataStructs.so.1.2023.09.3 lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/local/lib/libboost_system.so /usr/local/lib/libboost_serialization.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_serialization.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so -lpthread -ldl && :
[ 12% 79/640] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitAlignment.so.1.2023.09.3 lib/libRDKitAlignment.so.1 lib/libRDKitAlignment.so && :
[ 12% 80/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-l
ogical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -MF Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o.d -o Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp
[ 12% 81/640] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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 -DNDEBUG -fstack-protector-strong -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o lib/libRDKitEigenSolvers.so.1.2023.09.3 Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.build/lib:/usr/local/lib: lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/local/lib/libboost_system.so /usr/local/lib/libboost_serialization.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_serialization.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so -lpthread -ldl && :
[ 12% 82/640] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitEigenSolvers.so.1.2023.09.3 lib/libRDKitEigenSolvers.so.1 lib/libRDKitEigenSolvers.so && :
[ 12% 83/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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 -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -MF Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o.d -o Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/Numerics/Optimizer/BFGSOpt.cpp
[ 12% 84/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdAlignment_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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 -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -MF Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o.d -o Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp
[ 12% 85/640] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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 -DNDEBUG -fstack-protector-strong -pthread -shared -L/usr/local/lib -fstack-protector-strong -shared -o rdkit/Numerics/rdAlignment.so Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.build/lib:/usr/local/lib: lib/libRDKitAlignment.so.1.2023.09.3 lib/libRDKitRDBoost.so.1.2023.09.3 lib/libRDKitRDGeometryLib.so.1.2023.09.3 lib/libRDKitDataStructs.so.1.2023.09.3 /usr/local/lib/libpython3.9.so /usr/local/lib/libboost_python39.so lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/local/lib/libboost_system.so /usr/local/lib/libboost_serialization.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so /usr/local/lib/li
bboost_system.so /usr/local/lib/libboost_serialization.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_regex.so -lpthread -ldl && :
[ 13% 86/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical
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[ 13% 87/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logic
al-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/ForceField/ForceField.cpp
[ 13% 88/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logic
al-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -MF Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/ForceField/UFF/AngleBend.cpp
[ 13% 89/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logic
al-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -MF Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o.d -o Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/ForceField/UFF/BondStretch.cpp
[ 13% 90/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logic
al-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -MF Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o.d -o Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/ForceField/UFF/Nonbonded.cpp
[ 13% 91/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logic
al-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -MF Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/ForceField/UFF/Inversion.cpp
[ 14% 92/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logic
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op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/GraphMol/atomic_data.cpp
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op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/GraphMol/RWMol.cpp
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op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/GraphMol/Canon.cpp
FAILED: Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o
/usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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 -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/GraphMol/Canon.cpp
Assertion failed: (VDecl->isLinkageValid()), function DeduceVariableDeclarationType, file /usr/local/poudriere/jails/main-arm64/usr/src/contrib/llvm-project/clang/lib/Sema/SemaDecl.cpp, line 12822.
PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script.
Stack dump:
0. Program arguments: /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-l
ogical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/GraphMol/Canon.cpp
1. /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/GraphMol/Canon.cpp:84:2: current parser token ';'
2. /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/GraphMol/Canon.cpp:21:1: parsing namespace 'RDKit'
3. /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/GraphMol/Canon.cpp:22:1: parsing namespace 'RDKit::Canon'
#0 0x00000000057fac4c (/usr/bin/c+++0x57fac4c)
#1 0x00000000057f8f3c (/usr/bin/c+++0x57f8f3c)
#2 0x00000000057c2578 (/usr/bin/c+++0x57c2578)
#3 0x0000000089e8d13c (/lib/libthr.so.3+0x2b13c)
c++: error: clang frontend command failed with exit code 134 (use -v to see invocation)
FreeBSD clang version 17.0.6 (https://github.com/llvm/llvm-project.git llvmorg-17.0.6-0-g6009708b4367)
Target: aarch64-unknown-freebsd15.0
Thread model: posix
InstalledDir: /usr/bin
c++: note: diagnostic msg:
********************
PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
c++: note: diagnostic msg: /tmp/Canon-08b1f9.cpp
c++: note: diagnostic msg: /tmp/Canon-08b1f9.sh
c++: note: diagnostic msg:
********************
[ 20% 130/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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 -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/GraphMol/QueryOps.cpp
[ 20% 130/640] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.9 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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 -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_3/Code/GraphMol/MolPickler.cpp
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