From nobody Sun Sep 07 16:17:11 2025 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4cKZwm6cS1z66R4T for ; Sun, 07 Sep 2025 16:17:12 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R12" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4cKZwl5KKwz3kbC for ; Sun, 07 Sep 2025 16:17:11 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1757261831; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=pkMtAzfWlvpfVQ30eEjwQQ6PV2nF2BH6h4f/JuzDgj0=; b=Kd3P6FH3FEGTxAeK++eYoorjPmosaFk10seghdvHBAWo1FskKKoKv6Imtik86uiuoe9Gc3 sdSpGsxCw0yjBxAlw9swhi49S14hE2vLdiW+XzEcInnIb2ov5cKHEU3GeOVBIRe2enfgKY AmiCOE2LVMk9dIiElvF6dq2+70QQaYDfQZba1UCi7jUMihdznq2cWx6iEolVNmwMeJXbGQ ReUYNQIU41QHcIrcLVjtMECzA+6m5jYLEqsXLZ7dxkPHheErfIykmFdWx6Z2/mGx4UfndJ pUWBrdCwK55g+EuJS+WFvGZLXSxoVgP4MEz44Hziz5qCGbzxk7eNBZhOQOQuJA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1757261831; a=rsa-sha256; cv=none; b=OwLW/2yD/XgJ/cSKbp7hdS3cl+Gft/1Nd+9MCfIl9rfZ5QHGFBgsMppG1bL8paKU8bRPV5 7tykagmVcJwkWznogcE6XGKVKnYbk4G2RI4D1WruFE8VCF9gZSbG9d4dvrj+Ev4VZ/eDnZ q1KG0ESKydvZI+aDE1BkqaAqGviNvg/lnblt62/1D/jAAQ6/0sNoLL2IzwMK7Y1dj3yXxB 7LkszW4ep1AirRHZY9eDk5CE1sYAFK0sIPYM7e9QutR1ETho+UwXUAv9EiqYaf2Veo7IgF LbOWxN/R7PNPx/my9O+/XvRp/1HTHJSbNDMCZ0qmhpa88/bXFtZGx8omuWUhyw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none Received: from beefy18.nyi.freebsd.org (beefy18.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:21]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4cKZwl4QkdzC8r for ; Sun, 07 Sep 2025 16:17:11 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 23ab by beefy18.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy18.nyi.freebsd.org); Sun, 07 Sep 2025 16:17:11 +0000 To: yuri@FreeBSD.org Subject: [package - main-amd64-default][science/rdkit] Failed for rdkit-2025.03.1_2 in build Cc: pkg-fallout@FreeBSD.org Date: Sun, 07 Sep 2025 16:17:11 +0000 Message-Id: <68bdb007.23ab.51a7cbb7@beefy18.nyi.freebsd.org> From: List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@FreeBSD.org You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p118fb2971704_s4ab64e34911/logs/rdkit-2025.03.1_2.log Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p118fb2971704_s4ab64e34911 Log: =>> Building science/rdkit build started at Sun Sep 7 16:08:37 UTC 2025 port directory: /usr/ports/science/rdkit package name: rdkit-2025.03.1_2 building for: FreeBSD main-amd64-default-job-06 16.0-CURRENT FreeBSD 16.0-CURRENT 1600000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 3339 Sep 6 01:01 /usr/ports/science/rdkit/Makefile Ports top last git commit: 118fb297170 Ports top unclean checkout: no Port dir last git commit: b304d8ab18a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.3 Host OSVERSION: 1500061 Jail OSVERSION: 1600000 Job Id: 06 !!! Jail is newer than host. (Jail: 1600000, Host: 1500061) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1600000 UNAME_v=FreeBSD 16.0-CURRENT 1600000 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=3.4.3 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/06/.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-3.4.3 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-2025.03.1_2: DOCS=on: Build and/or install documentation PGSQL=off: Build the PostgreSQL cartridge PYTHON=on: Python bindings or support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" 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=2025.03.1 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-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> rdkit-2025.03.1_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.2.2.pkg [main-amd64-default-job-06] Installing pkg-2.2.2... [main-amd64-default-job-06] Extracting pkg-2.2.2: .......... done ===> rdkit-2025.03.1_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of rdkit-2025.03.1_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user => ComicNeue-Regular.ttf doesn't seem to exist in /portdistfiles/rdkit-2025.03.1. => Attempting to fetch http://distcache.FreeBSD.org/local-distfiles/yuri/ComicNeue-Regular.ttf ComicNeue-Regular.ttf 21 kB 104 MBps 00s => rdkit-rdkit-Release_2025_03_1_GH0.tar.gz doesn't seem to exist in /portdistfiles/rdkit-2025.03.1. => Attempting to fetch https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2025_03_1?dummy=/rdkit-rdkit-Release_2025_03_1_GH0.tar.gz fetch: https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2025_03_1?dummy=/rdkit-rdkit-Release_2025_03_1_GH0.tar.gz: size unknown fetch: https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2025_03_1?dummy=/rdkit-rdkit-Release_2025_03_1_GH0.tar.gz: size of remote file is not known rdkit-rdkit-Release_2025_03_1_GH0.tar.gz 78 MB 12 MBps 06s => rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz doesn't seem to exist in /portdistfiles/rdkit-2025.03.1. => Attempting to fetch https://codeload.github.com/rareylab/RingDecomposerLib/tar.gz/v1.1.3_rdkit?dummy=/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz fetch: https://codeload.github.com/rareylab/RingDecomposerLib/tar.gz/v1.1.3_rdkit?dummy=/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz: size unknown fetch: https://codeload.github.com/rareylab/RingDecomposerLib/tar.gz/v1.1.3_rdkit?dummy=/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz: size of remote file is not known rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz 134 kB 5152 kBps 00s => ncbi-pubchem-align3d-daefab3_GH0.tar.gz doesn't seem to exist in /portdistfiles/rdkit-2025.03.1. => Attempting to fetch https://codeload.github.com/ncbi/pubchem-align3d/tar.gz/daefab3?dummy=/ncbi-pubchem-align3d-daefab3_GH0.tar.gz fetch: https://codeload.github.com/ncbi/pubchem-align3d/tar.gz/daefab3?dummy=/ncbi-pubchem-align3d-daefab3_GH0.tar.gz: size unknown fetch: https://codeload.github.com/ncbi/pubchem-align3d/tar.gz/daefab3?dummy=/ncbi-pubchem-align3d-daefab3_GH0.tar.gz: size of remote file is not known ncbi-pubchem-align3d-daefab3_GH0.tar.gz 109 kB 4359 kBps 00s => aantron-better-enums-520d8ee_GH0.tar.gz doesn't seem to exist in /portdistfiles/rdkit-2025.03.1. => Attempting to fetch https://codeload.github.com/aantron/better-enums/tar.gz/520d8ee?dummy=/aantron-better-enums-520d8ee_GH0.tar.gz fetch: https://codeload.github.com/aantron/better-enums/tar.gz/520d8ee?dummy=/aantron-better-enums-520d8ee_GH0.tar.gz: size unknown fetch: https://codeload.github.com/aantron/better-enums/tar.gz/520d8ee?dummy=/aantron-better-enums-520d8ee_GH0.tar.gz: size of remote file is not known aantron-better-enums-520d8ee_GH0.tar.gz 133 kB 5285 kBps 00s ===> Fetching all distfiles required by rdkit-2025.03.1_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by rdkit-2025.03.1_2 for building => SHA256 Checksum OK for rdkit-2025.03.1/ComicNeue-Regular.ttf. => SHA256 Checksum OK for rdkit-2025.03.1/rdkit-rdkit-Release_2025_03_1_GH0.tar.gz. -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning at /usr/local/share/cmake/Modules/FetchContent.cmake:2111 (message): FETCHCONTENT_FULLY_DISCONNECTED is set to true, which requires the source directory for dependency Catch2 to already be populated. This generally means it must not be set to true the first time CMake is run in a build directory. The following source directory should already be populated, but it doesn't exist: /wrkdirs/usr/ports/science/rdkit/work/.build/_deps/catch2-src Policy CMP0170 controls enforcement of this requirement. Call Stack (most recent call first): /usr/local/share/cmake/Modules/FetchContent.cmake:2384 (__FetchContent_Populate) CMakeLists.txt:166 (FetchContent_MakeAvailable) -- Found Python3: /usr/local/bin/python3.11 (found version "3.11.13") found components: Interpreter Development.Module NumPy Python Install directory /usr/local/lib/python3.11/site-packages nbval not found, disabling the jupyter tests -- Found Eigen3: /usr/local/include/eigen3 (Required is at least version "2.91.0") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE == Using strict rotor definition -- maeparser include dir set as '/usr/local/include' -- maeparser libraries set as '/usr/local/lib/libmaeparser.so' -- coordgen include dir set as /usr/local/include -- coordgen libraries set as '/usr/local/lib/libcoordgen.so' -- Found RingDecomposerLib source in /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -- Found Python3: /usr/local/bin/python3.11 (found version "3.11.13") found components: Interpreter /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/Data/Fonts/ComicNeue-Regular.ttf already there, skipping the download -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) -- Found Cairo: /usr/local/include/cairo -- Found Freetype: /usr/local/lib/libfreetype.so (found version "2.13.3") -- Found RapidJSON source in /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/External -- Configuring done (5.0s) -- Generating done (0.9s) 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 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for rdkit-2025.03.1_2 [ 0% 3/692] /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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_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_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/External 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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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_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_03_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/Code -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -D_GNU_SOURCE -fstack-protecto r-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/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_03_1/Code/GraphMol/Canon.cpp 1. /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/Code/GraphMol/Canon.cpp:87:2: current parser token ';' 2. /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/Code/GraphMol/Canon.cpp:22:1: parsing namespace 'RDKit' 3. /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/Code/GraphMol/Canon.cpp:23:1: parsing namespace 'RDKit::Canon' #0 0x000020070cf9b4a9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x419b4a9) #1 0x000020070cf99215 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x4199215) #2 0x000020070cf42012 (/usr/lib/libprivatellvm.so.19+0x4142012) #3 0x0000200711fba97c (/lib/libthr.so.3+0x1a97c) #4 0x0000200711fb9f8b (/lib/libthr.so.3+0x19f8b) #5 0x0000200702d262d3 ([vdso]+0x2d3) #6 0x0000200715812b4a _thr_kill (/lib/libsys.so.7+0x19b4a) #7 0x00002007135fade4 raise (/lib/libc.so.7+0xc5de4) #8 0x00002007136ad359 abort (/lib/libc.so.7+0x178359) #9 0x00002007135ddb91 (/lib/libc.so.7+0xa8b91) #10 0x0000200706b4cb12 clang::Sema::DeduceVariableDeclarationType(clang::VarDecl*, bool, clang::Expr*) (/usr/lib/libprivateclang.so.19+0x354cb12) #11 0x0000200706b4d1ae clang::Sema::AddInitializerToDecl(clang::Decl*, clang::Expr*, bool) (/usr/lib/libprivateclang.so.19+0x354d1ae) #12 0x000020070679a395 clang::Parser::ParseDeclarationAfterDeclaratorAndAttributes(clang::Declarator&, clang::Parser::ParsedTemplateInfo const&, clang::Parser::ForRangeInit*) (/usr/lib/libprivateclang.so.19+0x319a395) #13 0x0000200706796ce4 clang::Parser::ParseDeclGroup(clang::ParsingDeclSpec&, clang::DeclaratorContext, clang::ParsedAttributes&, clang::Parser::ParsedTemplateInfo&, clang::SourceLocation*, clang::Parser::ForRangeInit*) (/usr/lib/libprivateclang.so.19+0x3196ce4) #14 0x000020070687a2a3 clang::Parser::ParseDeclOrFunctionDefInternal(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x327a2a3) #15 0x0000200706879a89 clang::Parser::ParseDeclarationOrFunctionDefinition(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x3279a89) #16 0x0000200706878850 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x3278850) #17 0x00002007067ba0ad clang::Parser::ParseInnerNamespace(llvm::SmallVector const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (/usr/lib/libprivateclang.so.19+0x31ba0ad) #18 0x00002007067b96df clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x31b96df) #19 0x00002007067956f6 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x31956f6) #20 0x0000200706878433 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x3278433) #21 0x00002007067ba0ad clang::Parser::ParseInnerNamespace(llvm::SmallVector const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (/usr/lib/libprivateclang.so.19+0x31ba0ad) #22 0x00002007067b96df clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x31b96df) #23 0x00002007067956f6 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x31956f6) #24 0x0000200706878433 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x3278433) #25 0x0000200706876818 clang::Parser::ParseTopLevelDecl(clang::OpaquePtr&, clang::Sema::ModuleImportState&) (/usr/lib/libprivateclang.so.19+0x3276818) #26 0x00002007067803ee clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x31803ee) #27 0x00002007065eebe2 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2feebe2) #28 0x000020070656122d clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2f6122d) #29 0x0000200706682605 clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x3082605) #30 0x00001ffee25a5051 (/usr/bin/c+++0xf051) #31 0x00001ffee25b32df (/usr/bin/c+++0x1d2df) #32 0x00002007062088ae (/usr/lib/libprivateclang.so.19+0x2c088ae) #33 0x000020070cf41d2c llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x4141d2c) #34 0x0000200706207efa clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x2c07efa) #35 0x00002007061c729e clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2bc729e) #36 0x00002007061c75ac clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2bc75ac) #37 0x00002007061e6390 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x2be6390) #38 0x00001ffee25b28f8 (/usr/bin/c+++0x1c8f8) #39 0x00001ffee25b0e72 (/usr/bin/c+++0x1ae72) #40 0x00002007135cf96f __libc_start1 (/lib/libc.so.7+0x9a96f) 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-647858.cpp c++: note: diagnostic msg: /tmp/Canon-647858.sh c++: note: diagnostic msg: ******************** [ 8% 59/692] /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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_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_03_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/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-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/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_03_1/Code/GraphMol/AtomIterators.cpp [ 8% 59/692] /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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_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_03_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/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-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_2025_03_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