=>> Building science/py-mmcif build started at Tue Apr 2 04:38:35 BST 2024 port directory: /usr/ports/science/py-mmcif package name: py39-mmcif-0.84 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 929 Jan 7 06:26 /usr/ports/science/py-mmcif/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 7f63d19af4 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 16 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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 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NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-mmcif-0.84 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> py39-mmcif-0.84 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py39-mmcif-0.84 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py39-mmcif-0.84 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py39-mmcif-0.84 for building => SHA256 Checksum OK for mmcif-0.84.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py39-mmcif-0.84 for building ===> Extracting for py39-mmcif-0.84 => SHA256 Checksum OK for mmcif-0.84.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for py39-mmcif-0.84 ===> Applying FreeBSD patches for py39-mmcif-0.84 from /usr/ports/science/py-mmcif/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-mmcif-0.84 depends on package: py39-future>0 - not found ===> Installing existing package /packages/All/py39-future-0.18.3.pkg [pkg-builder.dan.net.uk] Installing py39-future-0.18.3... [pkg-builder.dan.net.uk] `-- Installing py39-setuptools-63.1.0_1... [pkg-builder.dan.net.uk] | `-- Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] | | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] | | `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] | | `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing readline-8.2.10... 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[pkg-builder.dan.net.uk] | `-- Extracting py39-openssl-23.2.0,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting py39-urllib3-1.26.18,1: .......... done [pkg-builder.dan.net.uk] Extracting py39-requests-2.31.0: .......... done ===== Message from py39-urllib3-1.26.18,1: -- Since version 1.25 HTTPS connections are now verified by default which is done via "cert_reqs = 'CERT_REQUIRED'". While certificate verification can be disabled via "cert_reqs = 'CERT_NONE'", it's highly recommended to leave it on. Various consumers of net/py-urllib3 already have implemented routines that either explicitly enable or disable HTTPS certificate verification (e.g. via configuration settings, CLI arguments, etc.). Yet it may happen that there are still some consumers which don't explicitly enable/disable certificate verification for HTTPS connections which could then lead to errors (as is often the case with self-signed certificates). In case of an error one should try first to temporarily disable certificate verification of the problematic urllib3 consumer to see if that approach will remedy the issue. ===> py39-mmcif-0.84 depends on package: py39-requests>=2.25 - found ===> Returning to build of py39-mmcif-0.84 ===> py39-mmcif-0.84 depends on package: py39-six>0 - not found ===> Installing existing package /packages/All/py39-six-1.16.0.pkg [pkg-builder.dan.net.uk] Installing py39-six-1.16.0... [pkg-builder.dan.net.uk] Extracting py39-six-1.16.0: ....... done ===> py39-mmcif-0.84 depends on package: py39-six>0 - found ===> Returning to build of py39-mmcif-0.84 ===> py39-mmcif-0.84 depends on executable: cmake - not found ===> Installing existing package /packages/All/cmake-core-3.28.3.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.28.3... [pkg-builder.dan.net.uk] `-- Installing expat-2.6.1... 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[pkg-builder.dan.net.uk] `-- Extracting libtextstyle-0.22.3: .......... done [pkg-builder.dan.net.uk] `-- Installing m4-1.4.19_1,1... [pkg-builder.dan.net.uk] | `-- Installing libsigsegv-2.14... [pkg-builder.dan.net.uk] | `-- Extracting libsigsegv-2.14: ..... done [pkg-builder.dan.net.uk] `-- Extracting m4-1.4.19_1,1: .......... done [pkg-builder.dan.net.uk] Extracting bison-3.8.2_1,1: .......... done ===== Message from libsigsegv-2.14: -- Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ===> py39-mmcif-0.84 depends on executable: bison - found ===> Returning to build of py39-mmcif-0.84 ===> py39-mmcif-0.84 depends on package: py39-setuptools>=63.1.0 - found ===> py39-mmcif-0.84 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py39-mmcif-0.84 running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py39-mmcif-0.84 running build running build_py creating build creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39 creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif copying mmcif/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api copying mmcif/api/Method.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api copying mmcif/api/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api copying mmcif/api/DataCategoryTyped.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api copying mmcif/api/DictionaryApi.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api copying mmcif/api/PdbxContainers.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api copying mmcif/api/DictionaryInclude.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api copying mmcif/api/DataCategoryBase.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api copying mmcif/api/DataCategory.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api copying mmcif/api/MethodUtils.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api copying mmcif/api/DictMethodRunner.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api copying mmcif/api/DataCategoryFormatted.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/core copying mmcif/core/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/core creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io copying mmcif/io/PdbxWriter.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io copying mmcif/io/IoAdapterPy.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io copying mmcif/io/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io copying mmcif/io/PdbxReader.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io copying mmcif/io/BuildDictionaryExec.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io copying mmcif/io/IoAdapterBase.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io copying mmcif/io/CifFile.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io copying mmcif/io/IoAdapterCore.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io copying mmcif/io/BinaryCifReader.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io copying mmcif/io/BinaryCifWriter.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io copying mmcif/io/PdbxExceptions.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io running build_ext CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is Clang 14.0.5 -- The CXX compiler identification is Clang 14.0.5 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /ccache/libexec/ccache/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: /ccache/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:21 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/local/bin/python3.9 (found version "3.9.18") CMake Warning (dev) at CMakeLists.txt:22 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonLibs: /usr/local/lib/libpython3.9.so.1.0 (found version "3.9.18") -- Python include path set to /usr/local/include/python3.9 CMake Deprecation Warning at modules/pybind11/CMakeLists.txt:8 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- pybind11 v2.10.1 CMake Warning (dev) at modules/pybind11/tools/FindPythonLibsNew.cmake:98 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): modules/pybind11/tools/pybind11Tools.cmake:50 (find_package) modules/pybind11/tools/pybind11Common.cmake:180 (include) modules/pybind11/CMakeLists.txt:206 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/local/bin/python3.9 (found suitable version "3.9.18", minimum required is "3.6") -- Found PythonLibs: /usr/local/lib/libpython3.9.so.1.0 -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Performing Test HAS_FLTO_THIN -- Performing Test HAS_FLTO_THIN - Success -- Compiler flags -Wall -Wno-unused-variable -Wno-deprecated-declarations -Wno-register -DBIG_ENDIAN_PLATFORM -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -fno-common -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -flto -- ---CMAKE MODULE PATH - -- ---CMAKE SOURCE DIR - /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84 -- ---CMAKE PROJECT DIR - /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84 -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- Found BISON: /usr/local/bin/bison (found version "3.8.2") STATUS,---ALL DONE WITH CMAKE -- Configuring done (5.4s) -- Generating done (0.0s) -- Build files have been written to: /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84/build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39 [ 3%] Building CXX object CMakeFiles/common.dir/modules/cpp-common/src/RcsbPlatform.C.o [ 3%] Building CXX object CMakeFiles/tables.dir/modules/cpp-tables/src/ISTable.C.o [ 4%] Building CXX object CMakeFiles/common.dir/modules/cpp-common/src/RcsbFile.C.o [ 6%] Building CXX object CMakeFiles/common.dir/modules/cpp-common/src/BlockIO.C.o [ 8%] Building CXX object CMakeFiles/common.dir/modules/cpp-common/src/CifString.C.o [ 9%] Building CXX object CMakeFiles/common.dir/modules/cpp-common/src/Serializer.C.o [ 11%] Building CXX object CMakeFiles/common.dir/modules/cpp-common/src/GenString.C.o [ 13%] Building CXX object CMakeFiles/common.dir/modules/cpp-common/src/GenCont.C.o [ 14%] Building CXX object CMakeFiles/common.dir/modules/cpp-common/src/Exceptions.C.o [ 16%] Building CXX object CMakeFiles/tables.dir/modules/cpp-tables/src/ITTable.C.o [ 18%] Building CXX object CMakeFiles/common.dir/modules/cpp-common/src/DataInfo.C.o [ 19%] Building CXX object CMakeFiles/common.dir/modules/cpp-common/src/mapped_vector.C.o [ 21%] Building CXX object CMakeFiles/common.dir/modules/cpp-common/src/mapped_ptr_vector.C.o [ 22%] Building CXX object CMakeFiles/tables.dir/modules/cpp-tables/src/TTable.C.o [ 22%] Built target common [ 24%] Building C object CMakeFiles/regex.dir/modules/cc-regex/src/regcomp.c.o [ 26%] Building C object CMakeFiles/regex.dir/modules/cc-regex/src/regexec.c.o [ 27%] Building CXX object CMakeFiles/tables.dir/modules/cpp-tables/src/TableFile.C.o In file included from /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84/modules/cc-regex/src/regexec.c:46: /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84/modules/cc-regex/src/engine.c:251:17: warning: variable 'dp' set but not used [-Wunused-but-set-variable] register char *dp; ^ In file included from /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84/modules/cc-regex/src/regexec.c:95: /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84/modules/cc-regex/src/engine.c:251:17: warning: variable 'dp' set but not used [-Wunused-but-set-variable] register char *dp; ^ 2 warnings generated. [ 29%] Building C object CMakeFiles/regex.dir/modules/cc-regex/src/regerror.c.o [ 31%] Building C object CMakeFiles/regex.dir/modules/cc-regex/src/regfree.c.o [ 31%] Built target regex [ 32%] Building CXX object CMakeFiles/cif-file.dir/modules/cpp-cif-file/src/CifFile.C.o [ 32%] Built target tables [ 34%] Building CXX object CMakeFiles/cif-file-util.dir/modules/cpp-cif-file-util/src/CifFileUtil.C.o [ 36%] Building CXX object CMakeFiles/cif-file-util.dir/modules/cpp-cif-file-util/src/CifCorrector.C.o [ 36%] Built target cif-file-util [ 37%] Building CXX object CMakeFiles/dict-obj-file.dir/modules/cpp-dict-obj-file/src/DictObjFileCreator.C.o [ 39%] Building CXX object CMakeFiles/cif-file.dir/modules/cpp-cif-file/src/DicFile.C.o [ 40%] Building CXX object CMakeFiles/dict-obj-file.dir/modules/cpp-dict-obj-file/src/DictObjFileReader.C.o [ 42%] Building CXX object CMakeFiles/dict-obj-file.dir/modules/cpp-dict-obj-file/src/DictObjContInfo.C.o [ 44%] Building CXX object CMakeFiles/cif-file.dir/modules/cpp-cif-file/src/ParentChild.C.o [ 45%] Building CXX object CMakeFiles/dict-obj-file.dir/modules/cpp-dict-obj-file/src/DictObjCont.C.o [ 47%] Building CXX object CMakeFiles/cif-file.dir/modules/cpp-cif-file/src/CifParentChild.C.o [ 49%] Building CXX object CMakeFiles/dict-obj-file.dir/modules/cpp-dict-obj-file/src/DictObjFile.C.o [ 50%] Building CXX object CMakeFiles/dict-obj-file.dir/modules/cpp-dict-obj-file/src/DictDataInfo.C.o [ 52%] Building CXX object CMakeFiles/cif-file.dir/modules/cpp-cif-file/src/CifDataInfo.C.o [ 54%] Building CXX object CMakeFiles/dict-obj-file.dir/modules/cpp-dict-obj-file/src/DictParentChild.C.o [ 55%] Building CXX object CMakeFiles/cif-file.dir/modules/cpp-cif-file/src/CifExcept.C.o [ 55%] Built target cif-file [ 57%] [BISON][bisontarget1] Building parser with bison 3.8.2 [ 59%] [FLEX][flextarget1] Building scanner with flex 2.6.4 [ 60%] [BISON][bisontarget2] Building parser with bison 3.8.2 [ 62%] [FLEX][flextarget2] Building scanner with flex 2.6.4 [ 63%] Building CXX object CMakeFiles/cif-parser.dir/modules/cpp-cif-parser/src/CifFileReadDef.C.o [ 63%] Built target dict-obj-file [ 65%] Building CXX object CMakeFiles/cif-parser.dir/modules/cpp-cif-parser/src/CifScannerBase.C.o [ 67%] Building CXX object CMakeFiles/cif-parser.dir/modules/cpp-cif-parser/src/CifParserBase.C.o [ 68%] Building CXX object CMakeFiles/cif-parser.dir/modules/cpp-cif-parser/src/DICScannerBase.C.o [ 70%] Building CXX object CMakeFiles/cif-parser.dir/modules/cpp-cif-parser/src/DICParserBase.C.o [ 72%] Building C object CMakeFiles/cif-parser.dir/src/CifParser.c.o [ 73%] Building C object CMakeFiles/cif-parser.dir/src/DICParser.c.o [ 75%] Building C object CMakeFiles/cif-parser.dir/src/CifScanner.c.o [ 77%] Building C object CMakeFiles/cif-parser.dir/src/DICScanner.c.o [ 77%] Built target cif-parser [ 78%] Linking CXX static library lib/libmmciflib-all.a [ 78%] Built target mmciflib-all [ 80%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapCifDataInfo.cpp.o [ 81%] Building CXX object CMakeFiles/mmcif_reader_test_1.dir/modules/cpp-mmciflib-test/src/CifReader.C.o [ 83%] Linking CXX executable bin/mmcif_reader_test_1 [ 83%] Built target mmcif_reader_test_1 [ 85%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapCifFile.cpp.o [ 86%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapCifFileReadDef.cpp.o [ 88%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapCifFileUtil.cpp.o [ 90%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapDicFile.cpp.o [ 91%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapDictDataInfo.cpp.o [ 93%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapISTable.cpp.o [ 95%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapTableFile.cpp.o [ 96%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapmmciflib.cpp.o [ 98%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wraprcsb_types.cpp.o [100%] Linking CXX shared module /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84/build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/core/mmciflib.cpython-39.so [100%] Built target mmciflib ------------- setup.py ----------------- Extension source path /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84 CMAKE_ARGS ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84/build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/core', '-DPYTHON_EXECUTABLE=/usr/local/bin/python3.9', '-DPYTHON_LIBRARY=/usr/local/lib/libpython3.9.so.1.0', '-DPYTHON_INCLUDE_DIR=/usr/local/include/python3.9', '-DCMAKE_BUILD_TYPE=Release'] self.build_temp build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39 extdir /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84/build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/core ext.name mmcif.core.mmciflib sys.executable /usr/local/bin/python3.9 sys.exec_prefix /usr/local CXXFLAGS -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DVERSION_INFO=\"0.84\" =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-mmcif-0.84 depends on package: py39-future>0 - found ===> py39-mmcif-0.84 depends on package: py39-msgpack>0 - found ===> py39-mmcif-0.84 depends on package: py39-requests>=2.25 - found ===> py39-mmcif-0.84 depends on package: py39-six>0 - found ===> py39-mmcif-0.84 depends on package: py39-setuptools>=63.1.0 - found ===> py39-mmcif-0.84 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py39-mmcif-0.84 ===> Generating temporary packing list running install /usr/local/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running build_ext CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Warning (dev) at CMakeLists.txt:2 (project): Policy CMP0048 is not set: project() command manages VERSION variables. Run "cmake --help-policy CMP0048" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The following variable(s) would be set to empty: CMAKE_PROJECT_VERSION CMAKE_PROJECT_VERSION_MAJOR CMAKE_PROJECT_VERSION_MINOR CMAKE_PROJECT_VERSION_PATCH This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:21 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/local/bin/python3.9 (found version "3.9.18") CMake Warning (dev) at CMakeLists.txt:22 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Python include path set to /usr/local/include/python3.9 CMake Deprecation Warning at modules/pybind11/CMakeLists.txt:8 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- pybind11 v2.10.1 -- Compiler flags -Wall -Wno-unused-variable -Wno-deprecated-declarations -Wno-register -DBIG_ENDIAN_PLATFORM -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -fno-common -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -flto -- ---CMAKE MODULE PATH - -- ---CMAKE SOURCE DIR - /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84 -- ---CMAKE PROJECT DIR - /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84 STATUS,---ALL DONE WITH CMAKE -- Configuring done (1.8s) -- Generating done (8.2s) -- Build files have been written to: /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84/build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39 [ 18%] Built target common [ 24%] Built target tables [ 31%] Built target regex [ 40%] Built target cif-file [ 44%] Built target cif-file-util [ 55%] Built target dict-obj-file [ 77%] Built target cif-parser [ 78%] Built target mmciflib-all [ 81%] Built target mmcif_reader_test_1 [ 83%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapCifDataInfo.cpp.o [ 85%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapCifFile.cpp.o [ 86%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapCifFileReadDef.cpp.o [ 88%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapCifFileUtil.cpp.o [ 90%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapDicFile.cpp.o [ 91%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapDictDataInfo.cpp.o [ 93%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapISTable.cpp.o [ 95%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapTableFile.cpp.o [ 96%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wraprcsb_types.cpp.o [ 98%] Building CXX object CMakeFiles/mmciflib.dir/modules/cpp-core-mmciflib-wrapper-gen/src/wrapmmciflib.cpp.o [100%] Linking CXX shared module /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84/build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/core/mmciflib.cpython-39.so [100%] Built target mmciflib ------------- setup.py ----------------- Extension source path /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84 CMAKE_ARGS ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84/build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/core', '-DPYTHON_EXECUTABLE=/usr/local/bin/python3.9', '-DPYTHON_LIBRARY=/usr/local/lib/libpython3.9.so.1.0', '-DPYTHON_INCLUDE_DIR=/usr/local/include/python3.9', '-DCMAKE_BUILD_TYPE=Release'] self.build_temp build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39 extdir /wrkdirs/usr/ports/science/py-mmcif/work-py39/mmcif-0.84/build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/core ext.name mmcif.core.mmciflib sys.executable /usr/local/bin/python3.9 sys.exec_prefix /usr/local CXXFLAGS -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DVERSION_INFO=\"0.84\" running install_lib creating /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9 creating /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages creating /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif creating /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api/Method.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api/__init__.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api/DataCategoryTyped.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api/DictionaryApi.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api/PdbxContainers.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api/DictionaryInclude.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api/DataCategoryBase.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api/DataCategory.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api/MethodUtils.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api/DictMethodRunner.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/api/DataCategoryFormatted.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/__init__.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif creating /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/core copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/core/__init__.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/core copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/core/mmciflib.cpython-39.so -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/core creating /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io/PdbxWriter.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io/IoAdapterPy.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io/__init__.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io/PdbxReader.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io/BuildDictionaryExec.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io/IoAdapterBase.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io/CifFile.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io/IoAdapterCore.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io/BinaryCifReader.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io/BinaryCifWriter.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/mmcif/io/PdbxExceptions.py -> /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api/Method.py to Method.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api/DataCategoryTyped.py to DataCategoryTyped.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api/DictionaryApi.py to DictionaryApi.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api/PdbxContainers.py to PdbxContainers.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api/DictionaryInclude.py to DictionaryInclude.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api/DataCategoryBase.py to DataCategoryBase.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api/DataCategory.py to DataCategory.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api/MethodUtils.py to MethodUtils.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api/DictMethodRunner.py to DictMethodRunner.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/api/DataCategoryFormatted.py to DataCategoryFormatted.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/core/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io/PdbxWriter.py to PdbxWriter.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io/IoAdapterPy.py to IoAdapterPy.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io/PdbxReader.py to PdbxReader.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io/BuildDictionaryExec.py to BuildDictionaryExec.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io/IoAdapterBase.py to IoAdapterBase.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io/CifFile.py to CifFile.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io/IoAdapterCore.py to IoAdapterCore.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io/BinaryCifReader.py to BinaryCifReader.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io/BinaryCifWriter.py to BinaryCifWriter.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif/io/PdbxExceptions.py to PdbxExceptions.cpython-39.pyc writing byte-compilation script '/tmp/tmp4t0o5y2y.py' /usr/local/bin/python3.9 /tmp/tmp4t0o5y2y.py removing /tmp/tmp4t0o5y2y.py running install_egg_info running egg_info writing mmcif.egg-info/PKG-INFO writing dependency_links to mmcif.egg-info/dependency_links.txt writing entry points to mmcif.egg-info/entry_points.txt writing requirements to mmcif.egg-info/requires.txt writing top-level names to mmcif.egg-info/top_level.txt reading manifest file 'mmcif.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'mmcif.egg-info/SOURCES.txt' Copying mmcif.egg-info to /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/lib/python3.9/site-packages/mmcif-0.84-py3.9.egg-info running install_scripts Installing build_dict_cli script to /wrkdirs/usr/ports/science/py-mmcif/work-py39/stage/usr/local/bin writing list of installed files to '/wrkdirs/usr/ports/science/py-mmcif/work-py39/.PLIST.pymodtmp' ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/build_dict_cli --> bin/build_dict_cli-3.9 Link: @bin/build_dict_cli --> bin/build_dict_cli-3.9 ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-04-02T03:38:35+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=7f63d19af4' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for py39-mmcif-0.84 ===> Building py39-mmcif-0.84 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py39-mmcif-0.84 build of science/py-mmcif@py39 | py39-mmcif-0.84 ended at Tue Apr 2 04:53:34 BST 2024 build time: 00:15:00