[package - main-amd64-default][science/rdkit] Failed for rdkit-2025.03.1_2 in build
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Date: Sat, 27 Sep 2025 08:25:48 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/p53919f5dd30e_s5632b0d4628/logs/rdkit-2025.03.1_2.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p53919f5dd30e_s5632b0d4628
Log:
=>> Building science/rdkit
build started at Sat Sep 27 08:23:29 -00 2025
port directory: /usr/ports/science/rdkit
package name: rdkit-2025.03.1_2
building for: FreeBSD main-amd64-default-job-08 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: 53919f5dd30
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: 1600000
Jail OSVERSION: 1600000
Job Id: 08
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===> 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
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===> Use 'make config' to modify these settings
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=======================<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-2025.03.1_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.3.1.pkg
[main-amd64-default-job-08] Installing pkg-2.3.1...
[main-amd64-default-job-08] Extracting pkg-2.3.1: .......... done
===> rdkit-2025.03.1_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of rdkit-2025.03.1_2
===========================================================================
=======================<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-2025.03.1_2 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-2025.03.1_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.
=> SHA256 Checksum OK for rdkit-2025.03.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz.
=> SHA256 Checksum OK for rdkit-2025.03.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz.
=> SHA256 Checksum OK for rdkit-2025.03.1/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-2025.03.1_2 for building
===> Extracting for rdkit-2025.03.1_2
=> 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.
=> SHA256 Checksum OK for rdkit-2025.03.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz.
=> SHA256 Checksum OK for rdkit-2025.03.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz.
=> SHA256 Checksum OK for rdkit-2025.03.1/aantron-better-enums-520d8ee_GH0.tar.gz.
===========================================================================
=======================<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-2025.03.1_2
===> Applying FreeBSD patches for rdkit-2025.03.1_2 from /usr/ports/science/rdkit/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> rdkit-2025.03.1_2 depends on package: catch>0 - not found
===> Installing existing package /packages/All/catch-2.13.10_1.pkg
[main-amd64-default-job-08] Installing catch-2.13.10_1...
[main-amd64-default-job-08] Extracting catch-2.13.10_1: .......... done
===> rdkit-2025.03.1_2 depends on package: catch>0 - found
<snip>
-- 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 (4.5s)
-- Generating done (1.4s)
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-2025.03.1_2
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-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/ROMol.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/Code/GraphMol/ROMol.cpp
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-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/PeriodicTable.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/Code/GraphMol/PeriodicTable.cpp
[ 7% 56/692] /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/atomic_data.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_03_1/Code/GraphMol/atomic_data.cpp
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[ 8% 58/692] /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/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_2025_03_1/Code/GraphMol/QueryOps.cpp
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-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
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 -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-a
liasing -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
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 -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 0x000008200d99b4a9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x419b4a9)
#1 0x000008200d999215 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x4199215)
#2 0x000008200d942012 (/usr/lib/libprivatellvm.so.19+0x4142012)
#3 0x0000082001d8e97c (/lib/libthr.so.3+0x1a97c)
#4 0x0000082001d8df8b (/lib/libthr.so.3+0x19f8b)
#5 0x000008200158e2d3 ([vdso]+0x2d3)
#6 0x00000820137219ea thr_kill (/lib/libsys.so.7+0x199ea)
#7 0x00000820119c3f94 raise (/lib/libc.so.7+0xc5f94)
#8 0x0000082011a76539 abort (/lib/libc.so.7+0x178539)
#9 0x00000820119a6ca1 (/lib/libc.so.7+0xa8ca1)
#10 0x0000082006b4cb12 clang::Sema::DeduceVariableDeclarationType(clang::VarDecl*, bool, clang::Expr*) (/usr/lib/libprivateclang.so.19+0x354cb12)
#11 0x0000082006b4d1ae clang::Sema::AddInitializerToDecl(clang::Decl*, clang::Expr*, bool) (/usr/lib/libprivateclang.so.19+0x354d1ae)
#12 0x000008200679a395 clang::Parser::ParseDeclarationAfterDeclaratorAndAttributes(clang::Declarator&, clang::Parser::ParsedTemplateInfo const&, clang::Parser::ForRangeInit*) (/usr/lib/libprivateclang.so.19+0x319a395)
#13 0x0000082006796ce4 clang::Parser::ParseDeclGroup(clang::ParsingDeclSpec&, clang::DeclaratorContext, clang::ParsedAttributes&, clang::Parser::ParsedTemplateInfo&, clang::SourceLocation*, clang::Parser::ForRangeInit*) (/usr/lib/libprivateclang.so.19+0x3196ce4)
#14 0x000008200687a2a3 clang::Parser::ParseDeclOrFunctionDefInternal(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x327a2a3)
#15 0x0000082006879a89 clang::Parser::ParseDeclarationOrFunctionDefinition(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x3279a89)
#16 0x0000082006878850 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x3278850)
#17 0x00000820067ba0ad 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 0x00000820067b96df clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x31b96df)
#19 0x00000820067956f6 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x31956f6)
#20 0x0000082006878433 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x3278433)
#21 0x00000820067ba0ad 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 0x00000820067b96df clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x31b96df)
#23 0x00000820067956f6 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x31956f6)
#24 0x0000082006878433 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x3278433)
#25 0x0000082006876818 clang::Parser::ParseTopLevelDecl(clang::OpaquePtr<clang::DeclGroupRef>&, clang::Sema::ModuleImportState&) (/usr/lib/libprivateclang.so.19+0x3276818)
#26 0x00000820067803ee clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x31803ee)
#27 0x00000820065eebe2 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2feebe2)
#28 0x000008200656122d clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2f6122d)
#29 0x0000082006682605 clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x3082605)
#30 0x00000817e0a4c051 (/usr/bin/c+++0xf051)
#31 0x00000817e0a5a2df (/usr/bin/c+++0x1d2df)
#32 0x00000820062088ae (/usr/lib/libprivateclang.so.19+0x2c088ae)
#33 0x000008200d941d2c llvm::CrashRecoveryContext::RunSafely(llvm::function_ref<void ()>) (/usr/lib/libprivatellvm.so.19+0x4141d2c)
#34 0x0000082006207efa 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 0x00000820061c729e clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2bc729e)
#36 0x00000820061c75ac 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 0x00000820061e6390 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl<std::__1::pair<int, clang::driver::Command const*>>&) (/usr/lib/libprivateclang.so.19+0x2be6390)
#38 0x00000817e0a598f8 (/usr/bin/c+++0x1c8f8)
#39 0x00000817e0a57e72 (/usr/bin/c+++0x1ae72)
#40 0x0000082011998a7f __libc_start1 (/lib/libc.so.7+0x9aa7f)
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-8fd682.cpp
c++: note: diagnostic msg: /tmp/Canon-8fd682.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