From nobody Sun Feb 25 09:42:22 2024 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 4TjJgf6xGKz5C5jf for ; Sun, 25 Feb 2024 09:42:22 +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 "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4TjJgf4MX0z4hnQ for ; Sun, 25 Feb 2024 09:42:22 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1708854142; a=rsa-sha256; cv=none; b=UKLlJtCJlVwmtqy+L5Wj3MJEIs4+Q3LEU87v5dCAvOxBZ2+Kds85q+fLdW4ezAsvTkt3cM brXk1bVbDZX/v7j5h3XPUXaKJRexBxtg6J9D9w9bgdwoEzZMUQwgZ80+lMwdWCgfxvKaSs rn9xL50kRONaLVz/L16SGA+0G+qP1JoPhl66HX0fbR8uzYQ/Q8cqclFo1lGWkZPCPDt+Sb HsQ+UU/3Lor6+wrRqt7RidGG0jXFr4qT3tO6rMnLjDq9M0LND/Pz+Fyj64leXrgeEltiqV Wdu4wcFix5ryOMVsGB/w4K65A/b9JnVTkbign8rXbfsqxBs/Fr+LXkzRe2kUfQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1708854142; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=88+kVzdpmYODAbq/BsmCevrldYbo/+c5gThwxTcfaoI=; b=wARYQFDDqVZoNdkNfwOKrFpW2TSrQUxM5YZnVq8BY81gWL9VgqlxbMK0IhduIRddiWPKXp cgaByzYmbvF8DFLTZpZxTFVw5iQsWvQg8AzVJYw90y+kx9Cvwtb4rTNlb0+at5nvFHzQlA wK/Hzhos/y+9lztiYzfwboTkLvAAhWL5cYP5P9wFA87AKdWQcbhdy0Cufutof6PekJ0Pjh 4GYeeWo0w4QiQmJ9zytkVllQFZddLAbuZ8RNo4LulRNgKy7M/DzQX8D3VdMy7gjan8twh1 C/LkNuVhV420yoS8czdP9RJ80ZjfxXOw5S0UrUw6aYI6nt3SWIJlYISlDj1Wwg== 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 4TjJgf3QDPzfGk for ; Sun, 25 Feb 2024 09:42:22 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 902 by beefy18.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy18.nyi.freebsd.org); Sun, 25 Feb 2024 09:42:22 +0000 To: yuri@FreeBSD.org Subject: [package - main-amd64-default][science/rdkit] Failed for rdkit-2023.09.5 in build Cc: pkg-fallout@FreeBSD.org Date: Sun, 25 Feb 2024 09:42:22 +0000 Message-Id: <65db0b7e.902.5554d908@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/p43e3af5f5763_sf5f08e41aa/logs/rdkit-2023.09.5.log Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p43e3af5f5763_sf5f08e41aa Log: =>> Building science/rdkit build started at Sun Feb 25 09:38:24 UTC 2024 port directory: /usr/ports/science/rdkit package name: rdkit-2023.09.5 building for: FreeBSD main-amd64-default-job-08 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: 43e3af5f576 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: 08 !!! 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. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500014 UNAME_v=FreeBSD 15.0-CURRENT 1500014 UNAME_r=15.0-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=3.4.1-1-g1e9f97d6 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/08/.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-3.4.1-1-g1e9f97d6 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-2023.09.5: DOCS=on: Build and/or install documentation PGSQL=off: Build the PostgreSQL cartridge PYTHON=on: Python bindings or support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/science/rdkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/rdkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/rdkit/work/.cache HOME=/wrkdirs/usr/ports/science/rdkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/rdkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/rdkit/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --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=" -fstack-protector-strong " 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_I NSTALL_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=2023.09.5 PORTDOCS="" DOCS="" NO_DOCS="@comment " PGSQL="@comment " NO_PGSQL="" PYTHON="" NO_PYTHON="@comment " LITTLE_ENDIAN="" CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/RDKit" EXAMPLESDIR="share/examples/rdkit" DATADIR="share/RDKit" WWWDIR="www/rdkit" ETCDIR="etc/rdkit" --End PLIST_SUB-- --SUB_LIST-- DOCS="" NO_DOCS="@comment " PGSQL="@comment " NO_PGSQL="" PYTHON="" NO_PYTHON="@comment " PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/RDKit DOCSDIR=/usr/local/share/doc/RDKit EXAMPLESDIR=/usr/local/share/examples/rdkit WWWDIR=/usr/local/www/rdkit ETCDIR=/usr/local/etc/rdkit --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # 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 --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-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-08] Installing pkg-1.20.9_1... [main-amd64-default-job-08] 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 =========================================================================== =================================================== ===== 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 ===> Fetching all distfiles required by rdkit-2023.09.5 for building =========================================================================== =================================================== ===== 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. =========================================================================== =================================================== ===== 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 ===> 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 extracting: OFL.txt extracting: ComicNeue-Light.ttf extracting: ComicNeue-LightItalic.ttf extracting: ComicNeue-Regular.ttf extracting: ComicNeue-Italic.ttf extracting: ComicNeue-Bold.ttf extracting: ComicNeue-BoldItalic.ttf =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== 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 =========================================================================== =================================================== [ 0% 7/640] /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK 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-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 -Wno-array-bounds -fPIC -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -O2 -pipe -D_GNU_ SOURCE -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -pthread -MD -MT External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLgraph.c.o -MF External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLgraph.c.o.d -o External/RingFamilies/CMakeFiles/RingDecomposerLib.dir/RingDecomposerLib/src/RingDecomposerLib/RDLgraph.c.o -c 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-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 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-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% 131/640] /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 0x000000082c74a76f (/lib/libthr.so.3+0x1a76f) #4 0x000000082c749d2b (/lib/libthr.so.3+0x19d2b) #5 0x00000008283b12d3 ([vdso]+0x2d3) #6 0x000000082e23235a thr_kill (/lib/libsys.so.7+0x1b35a) #7 0x000000082f2829c4 _raise (/lib/libc.so.7+0xb89c4) #8 0x000000082f335f39 abort (/lib/libc.so.7+0x16bf39) #9 0x000000082f266361 (/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 0x000000082f257aaa __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-78791a.cpp c++: note: diagnostic msg: /tmp/Canon-78791a.sh c++: note: diagnostic msg: ******************** [ 20% 131/640] /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/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_2023_09_5/Code/GraphMol/AtomIterators.cpp [ 20% 131/640] /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