[package - main-amd64-default][science/rdkit] Failed for rdkit-2023.09.5 in build

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From: <pkg-fallout_at_FreeBSD.org>
Date: Tue, 27 Feb 2024 08:57:35 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/beefy18/data/main-amd64-default/p74acf3311b89_s8bfb23abf8/logs/rdkit-2023.09.5.log
Build URL:      https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p74acf3311b89_s8bfb23abf8
Log:

=>> Building science/rdkit
build started at Tue Feb 27 08:53:13 UTC 2024
port directory: /usr/ports/science/rdkit
package name: rdkit-2023.09.5
building for: FreeBSD main-amd64-default-job-13 15.0-CURRENT FreeBSD 15.0-CURRENT 1500014 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r--  1 root wheel 2540 Feb 17 01:01 /usr/ports/science/rdkit/Makefile
Ports top last git commit: 74acf3311b8
Ports top unclean checkout: no
Port dir last git commit: b0f5256f17a
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-1-g1e9f97d6
Host OSVERSION: 1500006
Jail OSVERSION: 1500014
Job Id: 13




!!! Jail is newer than host. (Jail: 1500014, Host: 1500006) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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=======================<phase: check-sanity   >============================
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=======================<phase: pkg-depends    >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   rdkit-2023.09.5 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.20.9_1.pkg
[main-amd64-default-job-13] Installing pkg-1.20.9_1...
[main-amd64-default-job-13] Extracting pkg-1.20.9_1: .......... done
===>   rdkit-2023.09.5 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of rdkit-2023.09.5
===========================================================================
=======================<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
===> Fetching all distfiles required by rdkit-2023.09.5 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-2023.09.5 for building
=> SHA256 Checksum OK for rdkit-2023.09.5/Comic_Neue.zip.
=> SHA256 Checksum OK for rdkit-2023.09.5/rdkit-rdkit-Release_2023_09_5_GH0.tar.gz.
=> SHA256 Checksum OK for rdkit-2023.09.5/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-2023.09.5 for building
===>  Extracting for rdkit-2023.09.5
=> SHA256 Checksum OK for rdkit-2023.09.5/Comic_Neue.zip.
=> SHA256 Checksum OK for rdkit-2023.09.5/rdkit-rdkit-Release_2023_09_5_GH0.tar.gz.
=> SHA256 Checksum OK for rdkit-2023.09.5/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz.
Archive:  /portdistfiles/rdkit-2023.09.5/Comic_Neue.zip
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 extracting: ComicNeue-Italic.ttf
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===========================================================================
=======================<phase: patch-depends  >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch          >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  Patching for rdkit-2023.09.5
===>  Applying FreeBSD patches for rdkit-2023.09.5 from /usr/ports/science/rdkit/files
===========================================================================
=======================<phase: build-depends  >============================
<snip>
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[  3% 25/640] : && /usr/bin/c++ -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -DNDEBUG  -fstack-protector-strong -shared -Wl,-soname,libRDKitga.so.1 -o lib/libRDKitga.so.1.2023.09.5 External/GA/CMakeFiles/ga.dir/ga/StringChromosome.cpp.o External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o External/GA/CMakeFiles/ga.dir/util/Util.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/libb
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[  5% 38/640] : && /usr/bin/c++ -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -DNDEBUG  -fstack-protector-strong -shared -Wl,-soname,libRDKitRDStreams.so.1 -o lib/libRDKitRDStreams.so.1.2023.09.5 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.1.2023.09.5  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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno
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[  6% 41/640] : && /usr/bin/c++ -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -DNDEBUG  -fstack-protector-strong -shared -Wl,-soname,libRDKitRDBoost.so.1 -o lib/libRDKitRDBoost.so.1.2023.09.5 Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o  -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.build/lib:/usr/local/lib:  lib/libRDKitRDGeneral.so.1.2023.09.5  /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  /usr/local/lib/libpython3.9.so  /usr/local/lib/libboost_pytho
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[  6% 42/640] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitRDBoost.so.1.2023.09.5  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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -W
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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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -W
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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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -W
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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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -W
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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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -W
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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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -W
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[  7% 50/640] /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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -W
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[  7% 51/640] /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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -W
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[  7% 52/640] /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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -W
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[  7% 53/640] : && /usr/bin/c++ -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -DNDEBUG  -fstack-protector-strong -shared -Wl,-soname,libRDKitDataStructs.so.1 -o lib/libRDKitDataStructs.so.1.2023.09.5 Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o Code/DataStructs/CMakeFiles/DataStructs
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[  8% 54/640] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitDataStructs.so.1.2023.09.5  lib/libRDKitDataStructs.so.1 lib/libRDKitDataStructs.so && :
[  8% 55/640] /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 -DrdBase_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-f
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[  8% 56/640] : && /usr/bin/c++ -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -DNDEBUG  -fstack-protector-strong  -pthread -shared -L/usr/local/lib  -fstack-protector-strong -shared  -o rdkit/rdBase.so Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o  -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.build/lib:/usr/local/lib:  lib/libRDKitRDBoost.so.1.2023.09.5  lib/libRDKitRDGeneral.so.1.2023.09.5  -ldl  /usr/local/lib/libpython3.9.so  /usr/local/lib/libboost_python39.so  -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/l
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[  8% 57/640] /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_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DcDataStructs_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function
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[  8% 58/640] /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_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DcDataStructs_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function
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[  8% 59/640] /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_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DcDataStructs_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function
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[  9% 60/640] /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_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DcDataStructs_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function
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[  9% 61/640] /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_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DcDataStructs_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function
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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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function
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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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function
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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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function
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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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function
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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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function
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[ 10% 72/640] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitRDGeometryLib.so.1.2023.09.5  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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -W
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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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -W
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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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -W
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[ 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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-st
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[ 11% 78/640] : && /usr/bin/c++ -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -DNDEBUG  -fstack-protector-strong -shared -Wl,-soname,libRDKitAlignment.so.1 -o lib/libRDKitAlignment.so.1.2023.09.5 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.1.2023.09.5  lib/libRDKitDataStructs.so.1.2023.09.5  lib/libRDKitRDGeneral.so.1.2023.09.5  /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/l
ocal/lib/libboost_regex.so  -lpthread  -ldl && :
[ 12% 79/640] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitAlignment.so.1.2023.09.5  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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -
fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -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_5/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp
[ 12% 81/640] : && /usr/bin/c++ -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -DNDEBUG  -fstack-protector-strong -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o lib/libRDKitEigenSolvers.so.1.2023.09.5 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.1.2023.09.5  /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.1.2023.09.5  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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-st
rict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -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_5/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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -
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[ 12% 85/640] : && /usr/bin/c++ -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -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.1.2023.09.5  lib/libRDKitRDBoost.so.1.2023.09.5  lib/libRDKitRDGeometryLib.so.1.2023.09.5  lib/libRDKitDataStructs.so.1.2023.09.5  /usr/local/lib/libpython3.9.so  /usr/local/lib/libboost_python39.so  lib/libRDKitRDGeneral.so.1.2023.09.5  /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 && :
[ 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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-st
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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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-
strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -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_5/Code/ForceField/UFF/AngleBend.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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-
strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -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_5/Code/ForceField/ForceField.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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-
strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -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_5/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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-
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[ 19% 128/640] /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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-str
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[ 19% 129/640] /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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-str
ict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -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_5/Code/GraphMol/RWMol.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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-str
ict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -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_5/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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -W
no-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -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_5/Code/GraphMol/Canon.cpp
Assertion failed: (VDecl->isLinkageValid()), function DeduceVariableDeclarationType, file /usr/local/poudriere/jails/main-amd64/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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -f
no-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -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_5/Code/GraphMol/Canon.cpp
1.	/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/Code/GraphMol/Canon.cpp:85:2: current parser token ';'
2.	/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/Code/GraphMol/Canon.cpp:22:1: parsing namespace 'RDKit'
3.	/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/Code/GraphMol/Canon.cpp:23:1: parsing namespace 'RDKit::Canon'
 #0 0x0000000005bafa71 (/usr/bin/c+++0x5bafa71)
 #1 0x0000000005badd85 (/usr/bin/c+++0x5badd85)
 #2 0x0000000005b7313b (/usr/bin/c+++0x5b7313b)
 #3 0x000000082ac5e76f (/lib/libthr.so.3+0x1a76f)
 #4 0x000000082ac5dd2b (/lib/libthr.so.3+0x19d2b)
 #5 0x00000008287a22d3 ([vdso]+0x2d3)
 #6 0x000000082f70a35a thr_kill (/lib/libsys.so.7+0x1b35a)
 #7 0x000000082e9829c4 _raise (/lib/libc.so.7+0xb89c4)
 #8 0x000000082ea35f39 abort (/lib/libc.so.7+0x16bf39)
 #9 0x000000082e966361 (/lib/libc.so.7+0x9c361)
#10 0x00000000040b9cc1 (/usr/bin/c+++0x40b9cc1)
#11 0x00000000040ba2e9 (/usr/bin/c+++0x40ba2e9)
#12 0x0000000003d5ef31 (/usr/bin/c+++0x3d5ef31)
#13 0x0000000003d5c35b (/usr/bin/c+++0x3d5c35b)
#14 0x0000000003cf3a98 (/usr/bin/c+++0x3cf3a98)
#15 0x0000000003cf3367 (/usr/bin/c+++0x3cf3367)
#16 0x0000000003cf22ad (/usr/bin/c+++0x3cf22ad)
#17 0x0000000003d36bb9 (/usr/bin/c+++0x3d36bb9)
#18 0x0000000003d36325 (/usr/bin/c+++0x3d36325)
#19 0x0000000003d5ae84 (/usr/bin/c+++0x3d5ae84)
#20 0x0000000003cf1e09 (/usr/bin/c+++0x3cf1e09)
#21 0x0000000003d36bb9 (/usr/bin/c+++0x3d36bb9)
#22 0x0000000003d36325 (/usr/bin/c+++0x3d36325)
#23 0x0000000003d5ae84 (/usr/bin/c+++0x3d5ae84)
#24 0x0000000003cf1e09 (/usr/bin/c+++0x3cf1e09)
#25 0x0000000003cf029a (/usr/bin/c+++0x3cf029a)
#26 0x0000000003cea85e (/usr/bin/c+++0x3cea85e)
#27 0x000000000365432f (/usr/bin/c+++0x365432f)
#28 0x00000000035ccdad (/usr/bin/c+++0x35ccdad)
#29 0x0000000003720f1d (/usr/bin/c+++0x3720f1d)
#30 0x0000000002a33899 (/usr/bin/c+++0x2a33899)
#31 0x0000000002a423dc (/usr/bin/c+++0x2a423dc)
#32 0x000000000345c4be (/usr/bin/c+++0x345c4be)
#33 0x0000000005b72ed9 (/usr/bin/c+++0x5b72ed9)
#34 0x000000000345baf4 (/usr/bin/c+++0x345baf4)
#35 0x000000000341f9fa (/usr/bin/c+++0x341f9fa)
#36 0x000000000341fcc8 (/usr/bin/c+++0x341fcc8)
#37 0x000000000343b801 (/usr/bin/c+++0x343b801)
#38 0x0000000002a41aa0 (/usr/bin/c+++0x2a41aa0)
#39 0x0000000002a3ecdf (/usr/bin/c+++0x2a3ecdf)
#40 0x000000082e957aaa __libc_start1 (/lib/libc.so.7+0x8daaa)
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: x86_64-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-5c2028.cpp
c++: note: diagnostic msg: /tmp/Canon-5c2028.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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-str
ict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -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_5/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_5/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2023_09_5/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_5/Code -I/usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-str
ict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing  -D_GNU_SOURCE  -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_5/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