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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/beefy24/data/main-amd64-default/pa48e645bda85_s8234c1899b/logs/rdkit-2025.09.1.log Build URL: https://pkg-status.freebsd.org/beefy24/build.html?mastername=main-amd64-default&build=pa48e645bda85_s8234c1899b Log: =>> Building science/rdkit build started at Tue Nov 4 06:14:41 -00 2025 port directory: /usr/ports/science/rdkit package name: rdkit-2025.09.1 building for: FreeBSD main-amd64-default-job-37 16.0-CURRENT FreeBSD 16.0-CURRENT 1600004 amd64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 4486 Nov 1 01:01 /usr/ports/science/rdkit/Makefile Ports top last git commit: a48e645bd Ports top unclean checkout: no Port dir last git commit: 160a45c50 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4 Host OSVERSION: 1600000 Jail OSVERSION: 1600004 Job Id: 37 !!! Jail is newer than host. (Jail: 1600004, Host: 1600000) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1600004 UNAME_v=FreeBSD 16.0-CURRENT 1600004 UNAME_r=16.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.4 MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/main-amd64-default/37/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for rdkit-2025.09.1: DOCS=on: Build and/or install documentation PGSQL=off: Build the PostgreSQL cartridge PYTHON=on: Python bindings or support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.11" 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 --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/science/rdkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/rdkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/rdkit/work/.cache HOME=/wrkdirs/usr/ports/science/rdkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/rdkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/rdkit/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/science/rdkit/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- SHLIB_VER=2025.09.1 PORTDOCS="" DOCS="" NO_DOCS="@comment " PGSQL="@comment " NO_PGSQL="" PYTHON="" NO_PYTHON="@comment " LITTLE_ENDIAN="" CMAKE_BUILD_TYPE="release" GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd16 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=16.0 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/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd16 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 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 --End SUB_LIST-- ---Begin make.conf--- # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --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-2025.09.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.3.1_1.pkg [main-amd64-default-job-37] Installing pkg-2.3.1_1... [main-amd64-default-job-37] Extracting pkg-2.3.1_1: .......... done ===> rdkit-2025.09.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of rdkit-2025.09.1 =========================================================================== =======================<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-2025.09.1 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-2025.09.1 for building => SHA256 Checksum OK for rdkit-2025.09.1/v1.3.3.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.1/v3.0.2.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.1/v1.0.10. => SHA256 Checksum OK for rdkit-2025.09.1/v1.1.0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.1/ComicNeue-Regular.ttf. => SHA256 Checksum OK for rdkit-2025.09.1/rdkit-rdkit-Release_2025_09_1_GH0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.1/aantron-better-enums-520d8ee_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-2025.09.1 for building ===> Extracting for rdkit-2025.09.1 => SHA256 Checksum OK for rdkit-2025.09.1/v1.3.3.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.1/v3.0.2.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.1/v1.0.10. => SHA256 Checksum OK for rdkit-2025.09.1/v1.1.0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.1/ComicNeue-Regular.ttf. => SHA256 Checksum OK for rdkit-2025.09.1/rdkit-rdkit-Release_2025_09_1_GH0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz. <snip> -- Looking for stdint.h - found -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for string.h -- Looking for string.h - found -- Looking for sys/stat.h -- Looking for sys/stat.h - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for getpagesize -- Looking for getpagesize - found -- Looking for bcopy -- Looking for bcopy - found -- Looking for memmove -- Looking for memmove - found -- Looking for mmap -- Looking for mmap - found -- HAVE_DLFXN_H="" -- HAVE_FCNTL_H="1" -- HAVE_INTTYPES_H="1" -- HAVE_MEMORY_H="1" -- HAVE_STDINT_H="1" -- HAVE_STDLIB_H="1" -- HAVE_STRINGS_H="1" -- HAVE_STRING_H="1" -- HAVE_SYS_STAT_H="1" -- HAVE_SYS_TYPES_H="1" -- HAVE_SYS_UNISTD_H="" -- HAVE_GETPAGESIZE="1" -- HAVE_BCOPY="1" -- HAVE_MEMMOVE="1" -- HAVE_MMAP="1" -- Looking for 4 include files stdlib.h, ..., float.h -- Looking for 4 include files stdlib.h, ..., float.h - found -- Looking for off_t -- Looking for off_t - not found -- Looking for size_t -- Looking for size_t - not found == expat turn off warnings as errors when building /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Data/Fonts/ComicNeue-Regular.ttf already there, skipping the download -- Found PkgConfig: /usr/local/bin/pkgconf (found version "2.4.3") -- Found Cairo: /usr/local/include/cairo -- Found Freetype: /usr/local/lib/libfreetype.so (found version "2.14.1") Downloading file:///portdistfiles/rdkit-2025.09.1/v1.1.0.tar.gz... -- Configuring done (8.1s) -- Generating done (0.5s) CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CATCH_DIR CMAKE_COLOR_MAKEFILE CMAKE_VERBOSE_MAKEFILE Python_ADDITIONAL_VERSIONS 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-2025.09.1 [ 0% 3/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB 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57/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -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_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -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++20 -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_2025_09_1/Code/GraphMol/RWMol.cpp [ 6% 58/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -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 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/usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -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_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -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++20 -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_2025_09_1/Code/GraphMol/Canon.cpp FAILED: [code=1] Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -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_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -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++20 -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_2025_09_1/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 12951. 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_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -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_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -m popcnt -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++20 -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_2025_09_1/Code/GraphMol/Canon.cpp 1. /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/Canon.cpp:87:2: current parser token ';' 2. /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/Canon.cpp:22:1: parsing namespace 'RDKit' 3. /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/Canon.cpp:23:1: parsing namespace 'RDKit::Canon' #0 0x0000285811d9b4a9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x419b4a9) #1 0x0000285811d99215 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x4199215) #2 0x0000285811d42012 (/usr/lib/libprivatellvm.so.19+0x4142012) #3 0x00002858167c899c (/lib/libthr.so.3+0x1a99c) #4 0x00002858167c7fab (/lib/libthr.so.3+0x19fab) #5 0x000028580747a2d3 ([vdso]+0x2d3) #6 0x000028581a739a9a __sys_thr_kill (/lib/libsys.so.7+0x19a9a) #7 0x00002858182440d4 _raise (/lib/libc.so.7+0xc60d4) #8 0x00002858182f5489 abort (/lib/libc.so.7+0x177489) #9 0x0000285818226cc1 (/lib/libc.so.7+0xa8cc1) #10 0x000028580b54cb12 clang::Sema::DeduceVariableDeclarationType(clang::VarDecl*, bool, clang::Expr*) (/usr/lib/libprivateclang.so.19+0x354cb12) #11 0x000028580b54d1ae clang::Sema::AddInitializerToDecl(clang::Decl*, clang::Expr*, bool) (/usr/lib/libprivateclang.so.19+0x354d1ae) #12 0x000028580b19a395 clang::Parser::ParseDeclarationAfterDeclaratorAndAttributes(clang::Declarator&, clang::Parser::ParsedTemplateInfo const&, clang::Parser::ForRangeInit*) (/usr/lib/libprivateclang.so.19+0x319a395) #13 0x000028580b196ce4 clang::Parser::ParseDeclGroup(clang::ParsingDeclSpec&, clang::DeclaratorContext, clang::ParsedAttributes&, clang::Parser::ParsedTemplateInfo&, clang::SourceLocation*, clang::Parser::ForRangeInit*) (/usr/lib/libprivateclang.so.19+0x3196ce4) #14 0x000028580b27a2a3 clang::Parser::ParseDeclOrFunctionDefInternal(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x327a2a3) #15 0x000028580b279a89 clang::Parser::ParseDeclarationOrFunctionDefinition(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x3279a89) #16 0x000028580b278850 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x3278850) #17 0x000028580b1ba0ad clang::Parser::ParseInnerNamespace(llvm::SmallVector<clang::Parser::InnerNamespaceInfo, 4u> const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (/usr/lib/libprivateclang.so.19+0x31ba0ad) #18 0x000028580b1b96df clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x31b96df) #19 0x000028580b1956f6 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x31956f6) #20 0x000028580b278433 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x3278433) #21 0x000028580b1ba0ad clang::Parser::ParseInnerNamespace(llvm::SmallVector<clang::Parser::InnerNamespaceInfo, 4u> const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (/usr/lib/libprivateclang.so.19+0x31ba0ad) #22 0x000028580b1b96df clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x31b96df) #23 0x000028580b1956f6 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x31956f6) #24 0x000028580b278433 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x3278433) #25 0x000028580b276818 clang::Parser::ParseTopLevelDecl(clang::OpaquePtr<clang::DeclGroupRef>&, clang::Sema::ModuleImportState&) (/usr/lib/libprivateclang.so.19+0x3276818) #26 0x000028580b1803ee clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x31803ee) #27 0x000028580afeebe2 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2feebe2) #28 0x000028580af6122d clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2f6122d) #29 0x000028580b082605 clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x3082605) #30 0x0000284fe57ca051 (/usr/bin/c+++0xf051) #31 0x0000284fe57d82df (/usr/bin/c+++0x1d2df) #32 0x000028580ac088ae (/usr/lib/libprivateclang.so.19+0x2c088ae) #33 0x0000285811d41d2c llvm::CrashRecoveryContext::RunSafely(llvm::function_ref<void ()>) (/usr/lib/libprivatellvm.so.19+0x4141d2c) #34 0x000028580ac07efa clang::driver::CC1Command::Execute(llvm::ArrayRef<std::__1::optional<llvm::StringRef>>, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>*, bool*) const (/usr/lib/libprivateclang.so.19+0x2c07efa) #35 0x000028580abc729e clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2bc729e) #36 0x000028580abc75ac clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl<std::__1::pair<int, clang::driver::Command const*>>&, bool) const (/usr/lib/libprivateclang.so.19+0x2bc75ac) #37 0x000028580abe6390 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl<std::__1::pair<int, clang::driver::Command const*>>&) (/usr/lib/libprivateclang.so.19+0x2be6390) #38 0x0000284fe57d78f8 (/usr/bin/c+++0x1c8f8) #39 0x0000284fe57d5e72 (/usr/bin/c+++0x1ae72) #40 0x0000285818218b0f __libc_start1 (/lib/libc.so.7+0x9ab0f) c++: error: clang frontend command failed with exit code 134 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd16.0 Thread model: posix InstalledDir: /usr/bin Build config: +assertions 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-d0667d.cpp c++: note: diagnostic msg: /tmp/Canon-d0667d.sh c++: note: diagnostic msg: ******************** [ 7% 59/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -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_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -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++20 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/AtomIterators.cpp [ 7% 59/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -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_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -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++20 -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_2025_09_1/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 making "build" in /usr/ports/science/rdkit
