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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/beefy19/data/144i386-quarterly/3a7a1297a515/logs/rdkit-2025.09.2_4.log Build URL: https://pkg-status.freebsd.org/beefy19/build.html?mastername=144i386-quarterly&build=3a7a1297a515 Log: =>> Building science/rdkit build started at Sun Oct 4 15:05:56 UTC 2026 port directory: /usr/ports/science/rdkit package name: rdkit-2025.09.2_4 building for: FreeBSD 144i386-quarterly-job-03 14.4-RELEASE-p10 FreeBSD 14.4-RELEASE-p10 i386 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 4940 Oct 4 01:01 /usr/ports/science/rdkit/Makefile Ports top last git commit: 3a7a1297a515552d4aef02f06cd5ee1a92ed4583 Ports top unclean checkout: no Port dir last git commit: 3a7a1297a515552d4aef02f06cd5ee1a92ed4583 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8-3-gd92fb7c0 Host OSVERSION: 1600022 Jail OSVERSION: 1404000 Job Id: 03 ---Begin Environment--- SHELL=/bin/sh BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 OSVERSION=1404000 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 UNAME_m=i386 UNAME_p=i386 UNAME_r=14.4-RELEASE-p10 LOCALBASE=/usr/local UNAME_v=FreeBSD 14.4-RELEASE-p10 USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.8-3-gd92fb7c0 MASTERMNT=/usr/local/poudriere/data/.m/144i386-quarterly/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/144i386-quarterly/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=144i386-quarterly SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/144i386-quarterly/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8-3-gd92fb7c0 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-2025.09.2_4: 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/python3.12" 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=2025.09.2 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/python3.12 PYTHON_LIBDIR=lib/python3.12 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.12/site-packages PYTHON_SUFFIX=312 PYTHON_BASESUFFIX=312 PYTHON_TAG=.cpython-312 PYTHON_SOABI=.cpython-312 PYTHON_VER=3.12 PYTHON_BASEVER=3.12 PYTHON_VERSION=python3.12 PYTHON2="@comment " PYTHON3="" OSREL=14.4 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/python3.12 PYTHON_LIBDIR=/usr/local/lib/python3.12 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.12/site-packages PYTHON_SUFFIX=312 PYTHON_BASESUFFIX=312 PYTHON_TAG=.cpython-312 PYTHON_SOABI=.cpython-312 PYTHON_VER=3.12 PYTHON_BASEVER=3.12 PYTHON_VERSION=python3.12 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 MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### #### # 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) 524288 stack size (kbytes, -s) 65536 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-2025.09.2_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.8.4.pkg [144i386-quarterly-job-03] Installing pkg-2.8.4... [144i386-quarterly-job-03] Extracting pkg-2.8.4: .......... done ===> rdkit-2025.09.2_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of rdkit-2025.09.2_4 =========================================================================== =======================<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-2025.09.2_4 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-2025.09.2_4 for building => SHA256 Checksum OK for rdkit-2025.09.2/v1.3.3.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.2/v3.0.2.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.2/v1.0.11. => SHA256 Checksum OK for rdkit-2025.09.2/v1.1.0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.2/ComicNeue-Regular.ttf. => SHA256 Checksum OK for rdkit-2025.09.2/rdkit-rdkit-Release_2025_09_2_GH0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.2/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.2/ncbi-pubchem-align3d-daefab3_GH0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.2/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-2025.09.2_4 for building ===> Extracting for rdkit-2025.09.2_4 => SHA256 Checksum OK for rdkit-2025.09.2/v1.3.3.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.2/v3.0.2.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.2/v1.0.11. => SHA256 Checksum OK for rdkit-2025.09.2/v1.1.0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.2/ComicNeue-Regular.ttf. => SHA256 Checksum OK for rdkit-2025.09.2/rdkit-rdkit-Release_2025_09_2_GH0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.2/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.2/ncbi-pubchem-align3d-daefab3_GH0.tar.gz. => SHA256 Checksum OK for rdkit-2025.09.2/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-2025.09.2_4 ===> Applying FreeBSD patches for rdkit-2025.09.2_4 from /usr/ports/science/rdkit/files =========================================================================== =======================<phase: build-depends >============================ <snip> [ 71% 574/804] : && /usr/bin/c++ -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -DNDEBUG -Xlinker --dependency-file=Code/RDBoost/CMakeFiles/RDBoost.dir/link.d -shared -Wl,-soname,libRDKitRDBoost.so.1 -o 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lib/libRDKitCatalogs.so.1.2025.09.2 lib/libRDKitGenericGroups.so.1.2025.09.2 lib/libRDKitGraphMol.so.1.2025.09.2 lib/libRDKitRDGeometryLib.so.1.2025.09.2 lib/libRDKitDataStructs.so.1.2025.09.2 lib/libRDKitRingDecomposerLib.so.1.2025.09.2 lib/libRDKitRDGeneral.so.1.2025.09.2 /usr/local/lib/libboost_serialization.so.1.92.0 /usr/local/lib/libboost_thread.so.1.92.0 /usr/local/lib/libboost_atomic.so.1.92.0 /usr/local/lib/libboost_chrono.so.1.92.0 /usr/local/lib/libboost_date_time.so.1.92.0 /usr/local/lib/libboost_container.so.1.92.0 /usr/local/lib/libboost_iostreams.so.1.92.0 /usr/local/lib/libboost_random.so.1.92.0 -lpthread -ldl && : [ 71% 577/804] : && /usr/bin/c++ -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -DNDEBUG -Xlinker 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-I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Ext ernal -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -isystem /usr/local/include/python3.12 -isystem /usr/local/include/eigen3 -isystem /usr/local/include -isystem /usr -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/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -MF Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o.d -o Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp FAILED: [code=1] Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_MATH_TR1_DYN_LINK -DBOOST_MATH_TR1_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdBase_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/External -I/wrkdir s/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -isystem /usr/local/include/python3.12 -isystem /usr/local/include/eigen3 -isystem /usr/local/include -isystem /usr -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/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -MF Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o.d -o Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp:10: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/python.h:5: In file included from /usr/local/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9: /usr/local/include/boost/python/suite/indexing/indexing_suite.hpp:296:37: error: no member named 'clear' in 'boost::python::detail::final_list_derived_policies<std::list<int>, true>' 296 | return DerivedPolicies::clear(container); | ~~~~~~~~~~~~~~~~~^ /usr/local/include/boost/python/suite/indexing/indexing_suite.hpp:187:32: note: in instantiation of member function 'boost::python::indexing_suite<std::list<int>, boost::python::detail::final_list_derived_policies<std::list<int>, true>, true>::base_clear' requested here 187 | .def("clear", &base_clear) | ^ /usr/local/include/boost/python/def_visitor.hpp:31:29: note: in instantiation of function template specialization 'boost::python::indexing_suite<std::list<int>, boost::python::detail::final_list_derived_policies<std::list<int>, true>, true>::visit<boost::python::class_<std::list<int>>>' requested here 31 | v.derived_visitor().visit(c); | ^ /usr/local/include/boost/python/def_visitor.hpp:67:29: note: in instantiation of function template specialization 'boost::python::def_visitor_access::visit<boost::python::def_visitor<boost::python::indexing_suite<std::list<int>, boost::python::detail::final_list_derived_policies<std::list<int>, true>, true>>, boost::python::class_<std::list<int>>>' requested here 67 | def_visitor_access::visit(*this, c); | ^ /usr/local/include/boost/python/class.hpp:221:17: note: in instantiation of function template specialization 'boost::python::def_visitor<boost::python::indexing_suite<std::list<int>, boost::python::detail::final_list_derived_policies<std::list<int>, true>, true>>::visit<boost::python::class_<std::list<int>>>' requested here 221 | visitor.visit(*this); | ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap.h:124:10: note: in instantiation of function template specialization 'boost::python::class_<std::list<int>>::def<boost::python::indexing_suite<std::list<int>, boost::python::detail::final_list_derived_policies<std::list<int>, true>, true>>' requested here 124 | .def(python::list_indexing_suite<std::list<T>, 1>()); | ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp:260:3: note: in instantiation of function template specialization 'RegisterListConverter<int>' requested here 260 | RegisterListConverter<int>(); | ^ In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp:10: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/python.h:5: In file included from /usr/local/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9: /usr/local/include/boost/python/suite/indexing/indexing_suite.hpp:296:37: error: no member named 'clear' in 'boost::python::detail::final_list_derived_policies<std::list<int>, false>' 296 | return DerivedPolicies::clear(container); | ~~~~~~~~~~~~~~~~~^ /usr/local/include/boost/python/suite/indexing/indexing_suite.hpp:187:32: note: in instantiation of member function 'boost::python::indexing_suite<std::list<int>, boost::python::detail::final_list_derived_policies<std::list<int>, false>>::base_clear' requested here 187 | .def("clear", &base_clear) | ^ /usr/local/include/boost/python/def_visitor.hpp:31:29: note: in instantiation of function template specialization 'boost::python::indexing_suite<std::list<int>, boost::python::detail::final_list_derived_policies<std::list<int>, false>>::visit<boost::python::class_<std::list<int>>>' requested here 31 | v.derived_visitor().visit(c); | ^ /usr/local/include/boost/python/def_visitor.hpp:67:29: note: in instantiation of function template specialization 'boost::python::def_visitor_access::visit<boost::python::def_visitor<boost::python::indexing_suite<std::list<int>, boost::python::detail::final_list_derived_policies<std::list<int>, false>>>, boost::python::class_<std::list<int>>>' requested here 67 | def_visitor_access::visit(*this, c); | ^ /usr/local/include/boost/python/class.hpp:221:17: note: in instantiation of function template specialization 'boost::python::def_visitor<boost::python::indexing_suite<std::list<int>, boost::python::detail::final_list_derived_policies<std::list<int>, false>>>::visit<boost::python::class_<std::list<int>>>' requested here 221 | visitor.visit(*this); | ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap.h:127:10: note: in instantiation of function template specialization 'boost::python::class_<std::list<int>>::def<boost::python::indexing_suite<std::list<int>, boost::python::detail::final_list_derived_policies<std::list<int>, false>>>' requested here 127 | .def(python::list_indexing_suite<std::list<T>>()); | ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp:260:3: note: in instantiation of function template specialization 'RegisterListConverter<int>' requested here 260 | RegisterListConverter<int>(); | ^ In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp:10: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/python.h:5: In file included from /usr/local/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9: /usr/local/include/boost/python/suite/indexing/indexing_suite.hpp:296:37: error: no member named 'clear' in 'boost::python::detail::final_list_derived_policies<std::list<std::vector<int>>, true>' 296 | return DerivedPolicies::clear(container); | ~~~~~~~~~~~~~~~~~^ /usr/local/include/boost/python/suite/indexing/indexing_suite.hpp:187:32: note: in instantiation of member function 'boost::python::indexing_suite<std::list<std::vector<int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<int>>, true>, true>::base_clear' requested here 187 | .def("clear", &base_clear) | ^ /usr/local/include/boost/python/def_visitor.hpp:31:29: note: in instantiation of function template specialization 'boost::python::indexing_suite<std::list<std::vector<int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<int>>, true>, true>::visit<boost::python::class_<std::list<std::vector<int>>>>' requested here 31 | v.derived_visitor().visit(c); | ^ /usr/local/include/boost/python/def_visitor.hpp:67:29: note: in instantiation of function template specialization 'boost::python::def_visitor_access::visit<boost::python::def_visitor<boost::python::indexing_suite<std::list<std::vector<int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<int>>, true>, true>>, boost::python::class_<std::list<std::vector<int>>>>' requested here 67 | def_visitor_access::visit(*this, c); | ^ /usr/local/include/boost/python/class.hpp:221:17: note: in instantiation of function template specialization 'boost::python::def_visitor<boost::python::indexing_suite<std::list<std::vector<int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<int>>, true>, true>>::visit<boost::python::class_<std::list<std::vector<int>>>>' requested here 221 | visitor.visit(*this); | ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap.h:124:10: note: in instantiation of function template specialization 'boost::python::class_<std::list<std::vector<int>>>::def<boost::python::indexing_suite<std::list<std::vector<int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<int>>, true>, true>>' requested here 124 | .def(python::list_indexing_suite<std::list<T>, 1>()); | ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp:261:3: note: in instantiation of function template specialization 'RegisterListConverter<std::vector<int>>' requested here 261 | RegisterListConverter<std::vector<int>>(); | ^ In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp:10: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/python.h:5: In file included from /usr/local/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9: /usr/local/include/boost/python/suite/indexing/indexing_suite.hpp:296:37: error: no member named 'clear' in 'boost::python::detail::final_list_derived_policies<std::list<std::vector<int>>, false>' 296 | return DerivedPolicies::clear(container); | ~~~~~~~~~~~~~~~~~^ /usr/local/include/boost/python/suite/indexing/indexing_suite.hpp:187:32: note: in instantiation of member function 'boost::python::indexing_suite<std::list<std::vector<int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<int>>, false>>::base_clear' requested here 187 | .def("clear", &base_clear) | ^ /usr/local/include/boost/python/def_visitor.hpp:31:29: note: in instantiation of function template specialization 'boost::python::indexing_suite<std::list<std::vector<int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<int>>, false>>::visit<boost::python::class_<std::list<std::vector<int>>>>' requested here 31 | v.derived_visitor().visit(c); | ^ /usr/local/include/boost/python/def_visitor.hpp:67:29: note: in instantiation of function template specialization 'boost::python::def_visitor_access::visit<boost::python::def_visitor<boost::python::indexing_suite<std::list<std::vector<int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<int>>, false>>>, boost::python::class_<std::list<std::vector<int>>>>' requested here 67 | def_visitor_access::visit(*this, c); | ^ /usr/local/include/boost/python/class.hpp:221:17: note: in instantiation of function template specialization 'boost::python::def_visitor<boost::python::indexing_suite<std::list<std::vector<int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<int>>, false>>>::visit<boost::python::class_<std::list<std::vector<int>>>>' requested here 221 | visitor.visit(*this); | ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap.h:127:10: note: in instantiation of function template specialization 'boost::python::class_<std::list<std::vector<int>>>::def<boost::python::indexing_suite<std::list<std::vector<int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<int>>, false>>>' requested here 127 | .def(python::list_indexing_suite<std::list<T>>()); | ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp:261:3: note: in instantiation of function template specialization 'RegisterListConverter<std::vector<int>>' requested here 261 | RegisterListConverter<std::vector<int>>(); | ^ In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp:10: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/python.h:5: In file included from /usr/local/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9: /usr/local/include/boost/python/suite/indexing/indexing_suite.hpp:296:37: error: no member named 'clear' in 'boost::python::detail::final_list_derived_policies<std::list<std::vector<unsigned int>>, true>' 296 | return DerivedPolicies::clear(container); | ~~~~~~~~~~~~~~~~~^ /usr/local/include/boost/python/suite/indexing/indexing_suite.hpp:187:32: note: in instantiation of member function 'boost::python::indexing_suite<std::list<std::vector<unsigned int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<unsigned int>>, true>, true>::base_clear' requested here 187 | .def("clear", &base_clear) | ^ /usr/local/include/boost/python/def_visitor.hpp:31:29: note: in instantiation of function template specialization 'boost::python::indexing_suite<std::list<std::vector<unsigned int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<unsigned int>>, true>, true>::visit<boost::python::class_<std::list<std::vector<unsigned int>>>>' requested here 31 | v.derived_visitor().visit(c); | ^ /usr/local/include/boost/python/def_visitor.hpp:67:29: note: in instantiation of function template specialization 'boost::python::def_visitor_access::visit<boost::python::def_visitor<boost::python::indexing_suite<std::list<std::vector<unsigned int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<unsigned int>>, true>, true>>, boost::python::class_<std::list<std::vector<unsigned int>>>>' requested here 67 | def_visitor_access::visit(*this, c); | ^ /usr/local/include/boost/python/class.hpp:221:17: note: in instantiation of function template specialization 'boost::python::def_visitor<boost::python::indexing_suite<std::list<std::vector<unsigned int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<unsigned int>>, true>, true>>::visit<boost::python::class_<std::list<std::vector<unsigned int>>>>' requested here 221 | visitor.visit(*this); | ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap.h:124:10: note: in instantiation of function template specialization 'boost::python::class_<std::list<std::vector<unsigned int>>>::def<boost::python::indexing_suite<std::list<std::vector<unsigned int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<unsigned int>>, true>, true>>' requested here 124 | .def(python::list_indexing_suite<std::list<T>, 1>()); | ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp:262:3: note: in instantiation of function template specialization 'RegisterListConverter<std::vector<unsigned int>>' requested here 262 | RegisterListConverter<std::vector<unsigned int>>(); | ^ In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp:10: In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/python.h:5: In file included from /usr/local/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9: /usr/local/include/boost/python/suite/indexing/indexing_suite.hpp:296:37: error: no member named 'clear' in 'boost::python::detail::final_list_derived_policies<std::list<std::vector<unsigned int>>, false>' 296 | return DerivedPolicies::clear(container); | ~~~~~~~~~~~~~~~~~^ /usr/local/include/boost/python/suite/indexing/indexing_suite.hpp:187:32: note: in instantiation of member function 'boost::python::indexing_suite<std::list<std::vector<unsigned int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<unsigned int>>, false>>::base_clear' requested here 187 | .def("clear", &base_clear) | ^ /usr/local/include/boost/python/def_visitor.hpp:31:29: note: in instantiation of function template specialization 'boost::python::indexing_suite<std::list<std::vector<unsigned int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<unsigned int>>, false>>::visit<boost::python::class_<std::list<std::vector<unsigned int>>>>' requested here 31 | v.derived_visitor().visit(c); | ^ /usr/local/include/boost/python/def_visitor.hpp:67:29: note: in instantiation of function template specialization 'boost::python::def_visitor_access::visit<boost::python::def_visitor<boost::python::indexing_suite<std::list<std::vector<unsigned int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<unsigned int>>, false>>>, boost::python::class_<std::list<std::vector<unsigned int>>>>' requested here 67 | def_visitor_access::visit(*this, c); | ^ /usr/local/include/boost/python/class.hpp:221:17: note: in instantiation of function template specialization 'boost::python::def_visitor<boost::python::indexing_suite<std::list<std::vector<unsigned int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<unsigned int>>, false>>>::visit<boost::python::class_<std::list<std::vector<unsigned int>>>>' requested here 221 | visitor.visit(*this); | ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap.h:127:10: note: in instantiation of function template specialization 'boost::python::class_<std::list<std::vector<unsigned int>>>::def<boost::python::indexing_suite<std::list<std::vector<unsigned int>>, boost::python::detail::final_list_derived_policies<std::list<std::vector<unsigned int>>, false>>>' requested here 127 | .def(python::list_indexing_suite<std::list<T>>()); | ^ /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/RDBoost/Wrap/RDBase.cpp:262:3: note: in instantiation of function template specialization 'RegisterListConverter<std::vector<unsigned int>>' requested here 262 | RegisterListConverter<std::vector<unsigned int>>(); | ^ 6 errors generated. [ 75% 608/804] /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_MATH_TR1_DYN_LINK -DBOOST_MATH_TR1_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DcDataStructs_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work /rdkit-Release_2025_09_2/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -isystem /usr/local/include/python3.12 -isystem /usr/local/include/eigen3 -isystem /usr/local/include -isystem /usr -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/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -MF Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /wrkd irs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code/DataStructs/Wrap/DiscreteValueVect.cpp [ 75% 608/804] /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_MATH_TR1_DYN_LINK -DBOOST_MATH_TR1_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DcDataStructs_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work /rdkit-Release_2025_09_2/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_2/Code -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -isystem /usr/local/include/python3.12 -isystem /usr/local/include/eigen3 -isystem /usr/local/include -isystem /usr -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/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -MF Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /wrkdirs/usr/port s/science/rdkit/work/rdkit-Release_2025_09_2/Code/DataStructs/Wrap/SparseIntVect.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
