=>> Building biology/py-python-libsbml build started at Fri Mar 29 23:19:40 GMT 2024 port directory: /usr/ports/biology/py-python-libsbml package name: py39-python-libsbml-5.20.1 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 768 Dec 8 03:45 /usr/ports/biology/py-python-libsbml/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 4135d03c4d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 15 ---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 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--End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-python-libsbml/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-python-libsbml/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/.cache HOME=/wrkdirs/usr/ports/biology/py-python-libsbml/work-py39 TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- CMAKE_BUILD_PARALLEL_LEVEL=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-python-libsbml/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-python-libsbml/work-py39 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===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-python-libsbml-5.20.1 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-python-libsbml-5.20.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py39-python-libsbml-5.20.1 =========================================================================== =================================================== ===== 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-python-libsbml-5.20.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py39-python-libsbml-5.20.1 for building => SHA256 Checksum OK for python-libsbml-5.20.1.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-python-libsbml-5.20.1 for building ===> Extracting for py39-python-libsbml-5.20.1 => SHA256 Checksum OK for python-libsbml-5.20.1.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-python-libsbml-5.20.1 ===> Applying FreeBSD patches for py39-python-libsbml-5.20.1 from /usr/ports/biology/py-python-libsbml/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-python-libsbml-5.20.1 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... [pkg-builder.dan.net.uk] `-- Extracting expat-2.6.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.5... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.5: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.48.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.48.0: .......... 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 rhash-1.4.4_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] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.28.3: .......... done ===> py39-python-libsbml-5.20.1 depends on executable: cmake - found ===> Returning to build of py39-python-libsbml-5.20.1 ===> py39-python-libsbml-5.20.1 depends on executable: swig - not found ===> Installing existing package /packages/All/swig-4.1.1.pkg [pkg-builder.dan.net.uk] Installing swig-4.1.1... [pkg-builder.dan.net.uk] `-- Installing pcre2-10.43... [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] `-- Extracting pcre2-10.43: .......... done [pkg-builder.dan.net.uk] Extracting swig-4.1.1: .......... done ===> py39-python-libsbml-5.20.1 depends on executable: swig - found ===> Returning to build of py39-python-libsbml-5.20.1 ===> py39-python-libsbml-5.20.1 depends on package: py39-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py39-setuptools-63.1.0_1.pkg [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 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] `-- Extracting python39-3.9.18_1: .......... done [pkg-builder.dan.net.uk] Extracting py39-setuptools-63.1.0_1: .......... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> py39-python-libsbml-5.20.1 depends on package: py39-setuptools>=63.1.0 - found ===> Returning to build of py39-python-libsbml-5.20.1 ===> py39-python-libsbml-5.20.1 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-python-libsbml-5.20.1 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source/config/libtool.m4 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source/configure ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_dependencies/libiconv/source/m4/libtool.m4 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_dependencies/libiconv/source/configure ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_dependencies/libiconv/source/libcharset/m4/libtool.m4 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_dependencies/libiconv/source/libcharset/configure ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_dependencies/libiconv/source/libcharset/build-aux/config.libpath ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_dependencies/libiconv/source/build-aux/config.rpath ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_dependencies/libiconv/source/build-aux/config.libpath Using libSBML from: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source Using VERSION.txt: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source/VERSION.txt Creating: python-libsbml Version is: 5.20.1 building for python: 3.9.18 (main, Mar 26 2024, 16:40:26) [Clang 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc1238 running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py39-python-libsbml-5.20.1 Using libSBML from: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source Using VERSION.txt: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source/VERSION.txt Creating: python-libsbml Version is: 5.20.1 building for python: 3.9.18 (main, Mar 26 2024, 16:40:26) [Clang 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc1238 running build running build_py running build_ext name: _libsbml.cpython-39.so build temp: build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39 extension name: _libsbml extension dir: build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/libsbml/_libsbml.cpython-39.so target_dir_path: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/libsbml target_lib_path: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/libsbml/_libsbml.cpython-39.so suffix: freebsd-13.2-RELEASE-p10-amd64-cpython-39 cwd: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1 name: _libsbml.cpython-39.so, tmp: build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39 compiling dependencies cmake /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_dependencies -DCMAKE_BUILD_TYPE=Release -DWITH_STATIC_RUNTIME=ON -DCMAKE_INSTALL_PREFIX=/wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64 -DWITH_BZIP2=ON -DWITH_CHECK=OFF -DWITH_EXPAT=ON -DWITH_XERCES=OFF -DWITH_ICONV=OFF -DWITH_LIBXML=OFF -- 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 -- Check for working C compiler: /ccache/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done CMake Deprecation Warning at expat/expat/CMakeLists.txt:36 (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. -- Looking for dlfcn.h -- Looking for dlfcn.h - found -- Looking for fcntl.h -- Looking for fcntl.h - found -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for memory.h -- Looking for memory.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for string.h -- Looking for string.h - found -- Looking for sys/stat.h -- Looking for sys/stat.h - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for getpagesize -- Looking for getpagesize - found -- Looking for mmap -- Looking for mmap - found -- Looking for getrandom -- Looking for getrandom - found -- Looking for arc4random_buf -- Looking for arc4random_buf - found -- Looking for 4 include files stdlib.h, ..., float.h -- Looking for 4 include files stdlib.h, ..., float.h - found -- Looking for off_t -- Looking for off_t - not found -- Looking for size_t -- Looking for size_t - not found -- Performing Test HAVE_SYSCALL_GETRANDOM -- Performing Test HAVE_SYSCALL_GETRANDOM - Success -- Performing Test FLAG_NO_STRICT_ALIASING -- Performing Test FLAG_NO_STRICT_ALIASING - Success -- Performing Test FLAG_VISIBILITY -- Performing Test FLAG_VISIBILITY - Success -- Looking for cos in m -- Looking for cos in m - found CMake Warning at /usr/local/share/cmake/Modules/CPack.cmake:507 (message): CPack.cmake has already been included!! Call Stack (most recent call first): expat/expat/CMakeLists.txt:795 (include) -- =========================================================================== -- -- Configuration -- Generator .................. Unix Makefiles -- Build type ................. Release -- Prefix ..................... /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64 -- Shared libraries ........... OFF -- Character type ............. char (UTF-8) -- Library name postfix ....... -- -- Build documentation ........ OFF -- Build examples ............. OFF -- Build fuzzers .............. OFF -- Build tests ................ OFF -- Build tools (xmlwf) ........ OFF -- Build pkg-config file ...... ON -- Install files .............. ON -- -- Features -- // Advanced options, changes not advised -- Attributes info .......... OFF -- Context bytes ............ 1024 -- DTD support .............. ON -- Large size ............... OFF -- Minimum size ............. OFF -- Namespace support ........ ON -- -- Entropy sources -- getrandom ................ 1 -- syscall SYS_getrandom .... 1 -- libbsd ................... OFF -- /dev/random .............. ON -- -- Continue with -- make -- sudo make install -- -- =========================================================================== -- Configuring done (7.3s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: WITH_ICONV -- Build files have been written to: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/build_dependencies_freebsd-13.2-RELEASE-p10-amd64 cmake --build . --target install --config Release -- [ 4%] Building C object bzip2/CMakeFiles/bz2.dir/blocksort.c.o [ 8%] Building C object bzip2/CMakeFiles/bz2.dir/bzlib.c.o [ 12%] Building C object bzip2/CMakeFiles/bz2.dir/compress.c.o [ 16%] Building C object bzip2/CMakeFiles/bz2.dir/crctable.c.o [ 20%] Building C object bzip2/CMakeFiles/bz2.dir/decompress.c.o [ 24%] Building C object bzip2/CMakeFiles/bz2.dir/huffman.c.o [ 28%] Building C object bzip2/CMakeFiles/bz2.dir/randtable.c.o [ 32%] Linking C static library libbz2.a [ 32%] Built target bz2 [ 36%] Building C object expat/expat/CMakeFiles/expat.dir/lib/xmlparse.c.o [ 40%] Building C object expat/expat/CMakeFiles/expat.dir/lib/xmlrole.c.o [ 44%] Building C object expat/expat/CMakeFiles/expat.dir/lib/xmltok.c.o [ 48%] Linking C static library libexpat.a [ 48%] Built target expat [ 52%] Building C object zlib/CMakeFiles/zlib.dir/source/adler32.c.o [ 56%] Building C object zlib/CMakeFiles/zlib.dir/source/compress.c.o [ 60%] Building C object zlib/CMakeFiles/zlib.dir/source/crc32.c.o [ 64%] Building C object zlib/CMakeFiles/zlib.dir/source/deflate.c.o [ 68%] Building C object zlib/CMakeFiles/zlib.dir/source/gzio.c.o [ 72%] Building C object zlib/CMakeFiles/zlib.dir/source/infback.c.o [ 76%] Building C object zlib/CMakeFiles/zlib.dir/source/inffast.c.o [ 80%] Building C object zlib/CMakeFiles/zlib.dir/source/inflate.c.o [ 84%] Building C object zlib/CMakeFiles/zlib.dir/source/inftrees.c.o [ 88%] Building C object zlib/CMakeFiles/zlib.dir/source/trees.c.o [ 92%] Building C object zlib/CMakeFiles/zlib.dir/source/uncompr.c.o [ 96%] Building C object zlib/CMakeFiles/zlib.dir/source/zutil.c.o [100%] Linking C static library libzlib.a [100%] Built target zlib Install the project... -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/lib/libbz2.a -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/include/bzlib.h -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/include/bzip2/bzlib.h -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/include/expat_config.h -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/lib/libexpat.a -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/include/expat.h -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/include/expat_external.h -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/lib/pkgconfig/expat.pc -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/share/doc/expat/AUTHORS -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/share/doc/expat/changelog -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/lib/cmake/expat-2.4.8/expat-config.cmake -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/lib/cmake/expat-2.4.8/expat-config-version.cmake -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/lib/cmake/expat-2.4.8/expat.cmake -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/lib/cmake/expat-2.4.8/expat-release.cmake -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/lib/libzlib.a -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/include/zconf.h -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/include/zlib.h -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/include/zlib/zconf.h -- Installing: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/include/zlib/zlib.h cmake /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source -DCMAKE_BUILD_TYPE=Release -DWITH_STATIC_RUNTIME=ON -DWITH_EXPAT=ON -DWITH_LIBXML=OFF -DWITH_SWIG=ON -DWITH_ZLIB=ON -DWITH_PYTHON=ON -DPYTHON_EXECUTABLE=/usr/local/bin/python3.9 -DPYTHON_INCLUDE_DIR=/usr/local/include/python3.9 -DENABLE_COMP=ON -DENABLE_FBC=ON -DENABLE_LAYOUT=ON -DENABLE_QUAL=ON -DENABLE_GROUPS=ON -DENABLE_MULTI=ON -DENABLE_RENDER=ON -DENABLE_DISTRIB=ON -DENABLE_SPATIAL=ON -DPYTHON_USE_DYNAMIC_LOOKUP=ON -DLIBSBML_DEPENDENCY_DIR=/wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64 -- 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 -- Check for working C compiler: /ccache/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Found SWIG: /usr/local/bin/swig (found version "4.1.1") -- Performing Test EXPAT_EXPAT_TEST -- Performing Test EXPAT_EXPAT_TEST - Success -- Found EXPAT: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/lib/libexpat.a (found version "2.4.8") -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so - found -- Found BZ2: /usr/lib/libbz2.so (found version "1.0.8") -- Looking for gzopen in /usr/lib/libz.so -- Looking for gzopen in /usr/lib/libz.so - found -- Looking for include file check.h -- Looking for include file check.h - not found -- Looking for include file expat.h -- Looking for include file expat.h - not found -- Looking for include file errno.h -- Looking for include file errno.h - found -- Looking for include file ieeefp.h -- Looking for include file ieeefp.h - found -- Looking for include file math.h -- Looking for include file math.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for include file float.h -- Looking for include file float.h - found -- Looking for sqrt in m -- Looking for sqrt in m - found CMake Warning (dev) at src/bindings/python/CMakeLists.txt:36 (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 src/bindings/python/CMakeLists.txt:41 (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 (found version "3.9.18") -- ---------------------------------------------------------------------- libSBML version 5.20.1 ---------------------------------------------------------------------- More information and the latest version are available online at https://sbml.org/software/libsbml/ Please report problems using the issue tracker at https://github.com/sbmlteam/libsbml/issues To contact the developers directly, email libsbml-team@googlegroups.com Configured on host 'pkg-builder.dan.net.uk' host type = FreeBSD host operating system = FreeBSD 13.2-RELEASE-p10 host CPU architecture = amd64 General build flags: CC = /ccache/libexec/ccache/cc CXX = /ccache/libexec/ccache/c++ CPPFLAGS = -DLINUX CFLAGS = -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fno-strict-aliasing -fPIC CXXFLAGS = -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fno-strict-aliasing -fPIC LDFLAGS = 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= ON -- SBML 'render' package = ON -- SBML 'req' package = OFF -- SBML 'spatial' package = ON -- -- Other potentially important settings: -- Compression support is enabled for .zip and .gz files -- Compression support is enabled for .bz2 files -- ---------------------------------------------------------------------- -- Configuring done (3.0s) -- Generating done (0.4s) CMake Warning: Manually-specified variables were not used by the project: WITH_STATIC_RUNTIME -- Build files have been written to: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39 cmake --build . --target binding_python_lib --config Release -- [ 0%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/comp/extension/CompExtension.cpp.o [ 0%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/comp/extension/CompModelPlugin.cpp.o [ 0%] Building CXX object 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src/CMakeFiles/sbml-static.dir/sbml/packages/distrib/sbml/ListOfUncertParameters.cpp.o [ 8%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/distrib/sbml/ListOfUncertainties.cpp.o [ 8%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/distrib/sbml/UncertParameter.cpp.o [ 8%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/distrib/sbml/UncertSpan.cpp.o [ 8%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/distrib/sbml/Uncertainty.cpp.o [ 10%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/distrib/util/AnnotationToDistribConverter.cpp.o [ 10%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/distrib/util/DistribToAnnotationConverter.cpp.o /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source/src/sbml/packages/distrib/util/DistribToAnnotationConverter.cpp:242:11: warning: 144 enumeration values not handled in switch: 'AST_TIMES', 'AST_PLUS', 'AST_MINUS'... [-Wswitch] switch (type) { ^~~~ /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source/src/sbml/packages/distrib/util/DistribToAnnotationConverter.cpp:299:11: warning: 144 enumeration values not handled in switch: 'AST_TIMES', 'AST_PLUS', 'AST_MINUS'... [-Wswitch] switch (type) { ^~~~ 2 warnings generated. [ 10%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/distrib/validator/DistribConsistencyValidator.cpp.o [ 10%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/distrib/validator/DistribIdentifierConsistencyValidator.cpp.o [ 10%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/distrib/validator/DistribValidator.cpp.o [ 10%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/distrib/validator/constraints/DistribConsistencyConstraints.cpp.o [ 10%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/distrib/validator/constraints/DistribIdentifierConsistencyConstraints.cpp.o [ 10%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/fbc/extension/FbcExtension.cpp.o [ 10%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/fbc/extension/FbcModelPlugin.cpp.o [ 10%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/fbc/extension/FbcReactionPlugin.cpp.o [ 12%] Building CXX 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[ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/ExpatParser.cpp.o [100%] Linking CXX static library libsbml-static.a [100%] Built target sbml-static [100%] Swig Python source /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source/src/bindings/python/doc-converter/rewrite_pydoc.py:122: DeprecationWarning: the formatter module is deprecated from formatter import NullWriter, AbstractFormatter Warning: unable to expand @htmlinclude 'pkg-marker-Distrib.html' Warning: unable to expand @htmlinclude 'pkg-marker-l3v2extendedmath.html' Warning: unable to expand @htmlinclude 'pkg-marker-l3v2extendedmath.html' Warning: unable to expand @htmlinclude 'pkg-marker-l3v2extendedmath.html' Warning: unable to expand @htmlinclude 'pkg-marker-l3v2extendedmath.html' /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source/src/bindings/python/../swig/std_set.i:65: Warning 314: 'del' is a python keyword, renaming to '_del' /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source/src/bindings/python/../swig/std_set.i:65: Warning 314: 'del' is a python keyword, renaming to '_del' Python: Add Version to generated file -- Patching Python wrapper [100%] Built target binding_python_swig [100%] Building CXX object src/bindings/python/CMakeFiles/binding_python_lib.dir/libsbml_wrap.cpp.o [100%] Linking CXX shared library _libsbml.so [100%] Built target binding_python_lib copying pyd file to output file =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-python-libsbml-5.20.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-python-libsbml-5.20.1 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py39-python-libsbml-5.20.1 ===> Generating temporary packing list Using libSBML from: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source Using VERSION.txt: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source/VERSION.txt Creating: python-libsbml Version is: 5.20.1 building for python: 3.9.18 (main, Mar 26 2024, 16:40:26) [Clang 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc1238 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 name: _libsbml.cpython-39.so build temp: build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39 extension name: _libsbml extension dir: build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/libsbml/_libsbml.cpython-39.so target_dir_path: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/libsbml target_lib_path: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/libsbml/_libsbml.cpython-39.so suffix: freebsd-13.2-RELEASE-p10-amd64-cpython-39 cwd: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1 name: _libsbml.cpython-39.so, tmp: build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39 compiling dependencies cmake /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/libsbml_source -DCMAKE_BUILD_TYPE=Release -DWITH_STATIC_RUNTIME=ON -DWITH_EXPAT=ON -DWITH_LIBXML=OFF -DWITH_SWIG=ON -DWITH_ZLIB=ON -DWITH_PYTHON=ON -DPYTHON_EXECUTABLE=/usr/local/bin/python3.9 -DPYTHON_INCLUDE_DIR=/usr/local/include/python3.9 -DENABLE_COMP=ON -DENABLE_FBC=ON -DENABLE_LAYOUT=ON -DENABLE_QUAL=ON -DENABLE_GROUPS=ON -DENABLE_MULTI=ON -DENABLE_RENDER=ON -DENABLE_DISTRIB=ON -DENABLE_SPATIAL=ON -DPYTHON_USE_DYNAMIC_LOOKUP=ON -DLIBSBML_DEPENDENCY_DIR=/wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64 -- Check for working C compiler: /ccache/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done CMake Warning (dev) at src/bindings/python/CMakeLists.txt:36 (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. CMake Warning (dev) at src/bindings/python/CMakeLists.txt:41 (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. -- ---------------------------------------------------------------------- libSBML version 5.20.1 ---------------------------------------------------------------------- More information and the latest version are available online at https://sbml.org/software/libsbml/ Please report problems using the issue tracker at https://github.com/sbmlteam/libsbml/issues To contact the developers directly, email libsbml-team@googlegroups.com Configured on host 'pkg-builder.dan.net.uk' host type = FreeBSD host operating system = FreeBSD 13.2-RELEASE-p10 host CPU architecture = amd64 General build flags: CC = /ccache/libexec/ccache/cc CXX = /ccache/libexec/ccache/c++ CPPFLAGS = -DLINUX CFLAGS = -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fno-strict-aliasing -fPIC CXXFLAGS = -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fno-strict-aliasing -fPIC LDFLAGS = -fstack-protector-strong XML parser library configuration: XML library = expat CPPFLAGS for XML = -I/wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/include LIBS for XML = /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/install_dependencies_freebsd-13.2-RELEASE-p10-amd64/lib/libexpat.a Other libSBML configuration settings: Installation $prefix = /usr/local -- Value of $LD_LIBRARY_PATH = -- Using SWIG = /usr/local/bin/swig (Version 4.1.1) -- Using Python = /usr/local/bin/python3.9 -- Using C++ namespace ('libsbml') = no -- -- Build examples = no -- -- -- Support for SBML Level 3 Packages: -- SBML 'arrays' package = OFF -- SBML 'comp' package = ON -- SBML 'distrib' package = ON -- SBML 'dyn' package = OFF -- SBML 'fbc' package = ON -- SBML 'groups' package = ON -- SBML 'l3v2extendedmath' package = ON -- SBML 'layout' package = ON -- SBML 'multi' package = ON -- SBML 'qual' package = ON -- SBML 'render' package = ON -- SBML 'req' package = OFF -- SBML 'spatial' package = ON -- -- Other potentially important settings: -- Compression support is enabled for .zip and .gz files -- Compression support is enabled for .bz2 files -- ---------------------------------------------------------------------- -- Configuring done (10.8s) -- Generating done (7.0s) -- Build files have been written to: /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/python-libsbml-5.20.1/build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39 cmake --build . --target binding_python_lib --config Release -- [100%] Built target sbml-static [100%] Built target binding_python_swig [100%] Building CXX object src/bindings/python/CMakeFiles/binding_python_lib.dir/libsbml_wrap.cpp.o [100%] Linking CXX shared library _libsbml.so [100%] Built target binding_python_lib copying pyd file to output file running install_lib creating /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/stage/usr/local/lib/python3.9 creating /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/stage/usr/local/lib/python3.9/site-packages creating /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/stage/usr/local/lib/python3.9/site-packages/libsbml copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/libsbml/_libsbml.cpython-39.so -> /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/stage/usr/local/lib/python3.9/site-packages/libsbml copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/libsbml/__init__.py -> /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/stage/usr/local/lib/python3.9/site-packages/libsbml byte-compiling /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/stage/usr/local/lib/python3.9/site-packages/libsbml/__init__.py to __init__.cpython-39.pyc writing byte-compilation script '/tmp/tmp969nuugz.py' /usr/local/bin/python3.9 /tmp/tmp969nuugz.py removing /tmp/tmp969nuugz.py running install_egg_info running egg_info writing python_libsbml.egg-info/PKG-INFO writing dependency_links to python_libsbml.egg-info/dependency_links.txt writing top-level names to python_libsbml.egg-info/top_level.txt reading manifest file 'python_libsbml.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.html' adding license file 'LICENSE.txt' writing manifest file 'python_libsbml.egg-info/SOURCES.txt' Copying python_libsbml.egg-info to /wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/stage/usr/local/lib/python3.9/site-packages/python_libsbml-5.20.1-py3.9.egg-info running install_scripts writing list of installed files to '/wrkdirs/usr/ports/biology/py-python-libsbml/work-py39/.PLIST.pymodtmp' ====> 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=2024-03-29T23:19:40+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=4135d03c4d' '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-python-libsbml-5.20.1 ===> Building py39-python-libsbml-5.20.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py39-python-libsbml-5.20.1 build of biology/py-python-libsbml@py39 | py39-python-libsbml-5.20.1 ended at Sat Mar 30 03:35:43 GMT 2024 build time: 04:16:04