------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 FLAVOR=py39 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/construction/biology/py-python-libsbml XDG_CONFIG_HOME=/construction/biology/py-python-libsbml XDG_CACHE_HOME=/construction/biology/py-python-libsbml/.cache HOME=/construction/biology/py-python-libsbml TMPDIR="/tmp" PATH=/construction/biology/py-python-libsbml/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/py-python-libsbml/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/py-python-libsbml XDG_CONFIG_HOME=/construction/biology/py-python-libsbml XDG_CACHE_HOME=/construction/biology/py-python-libsbml/.cache HOME=/construction/biology/py-python-libsbml TMPDIR="/tmp" PATH=/construction/biology/py-python-libsbml/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/py-python-libsbml/.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 CCVER=gcc80 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/py-python-libsbml/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/python-libsbml" EXAMPLESDIR="share/examples/python-libsbml" DATADIR="share/python-libsbml" WWWDIR="www/python-libsbml" ETCDIR="etc/python-libsbml" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/python-libsbml DOCSDIR=/usr/local/share/doc/python-libsbml EXAMPLESDIR=/usr/local/share/examples/python-libsbml WWWDIR=/usr/local/www/python-libsbml ETCDIR=/usr/local/etc/python-libsbml SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/expat-2.5.0.pkg Installing /packages/All/libuv-1.46.0.pkg Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/openssl-1.1.1u,1.pkg Installing /packages/All/rhash-1.4.3.pkg Installing /packages/All/pkg-1.19.2.pkg Installing /packages/All/liblz4-1.9.4,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/zstd-1.5.5.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libarchive-3.6.2,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/ncurses-6.4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/cmake-core-3.26.1_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/pcre2-10.42.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/swig-4.1.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libffi-3.4.4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/mpdecimal-2.5.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/readline-8.2.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/python39-3.9.17.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from python39-3.9.17: -- 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 Installing /packages/All/py39-setuptools-63.1.0_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/ccache-3.7.12_4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. SUCCEEDED 00:00:17 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py39-python-libsbml-5.20.1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py39-python-libsbml-5.20.1 depends on file: /usr/local/sbin/pkg - found => python-libsbml-5.20.1.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://github.com/sbmlteam/python-libsbml/releases/download/v5.20.1/python-libsbml-5.20.1.tar.gz python-libsbml-5.20.1.tar.gz 0% of 46 MB 0 Bps python-libsbml-5.20.1.tar.gz 28% of 46 MB 44 MBps python-libsbml-5.20.1.tar.gz 46 MB 45 MBps 01s ===> Fetching all distfiles required by py39-python-libsbml-5.20.1 for building SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py39-python-libsbml-5.20.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-python-libsbml-5.20.1 for building => SHA256 Checksum OK for python-libsbml-5.20.1.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py39-python-libsbml-5.20.1 depends on file: /usr/local/sbin/pkg - found ===> 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. Extracted Memory Use: 285.41M SUCCEEDED 00:00:09 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py39-python-libsbml-5.20.1 ===> Applying ports patches for py39-python-libsbml-5.20.1 from /xports/biology/py-python-libsbml/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py39-python-libsbml-5.20.1 depends on executable: cmake - found ===> py39-python-libsbml-5.20.1 depends on executable: swig - found ===> 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 ===> py39-python-libsbml-5.20.1 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py39-python-libsbml-5.20.1 depends on executable: cmake - found ===> py39-python-libsbml-5.20.1 depends on executable: swig - found ===> 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 ===> py39-python-libsbml-5.20.1 depends on file: /usr/local/bin/ccache - found ===> Configuring for py39-python-libsbml-5.20.1 Using libSBML from: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source Using VERSION.txt: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/VERSION.txt Creating: python-libsbml Version is: 5.20.1 building for python: 3.9.17 (main, Jul 29 2023, 01:53:50) [GCC 8.3 [DragonFly] Release/2019-02-22] running config SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py39-python-libsbml-5.20.1 Using libSBML from: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source Using VERSION.txt: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/VERSION.txt Creating: python-libsbml Version is: 5.20.1 building for python: 3.9.17 (main, Jul 29 2023, 01:53:50) [GCC 8.3 [DragonFly] Release/2019-02-22] running build running build_py running build_ext name: _libsbml.cpython-39.so build temp: build/temp.dragonfly-6.5-x86_64-cpython-39 extension name: _libsbml extension dir: build/lib.dragonfly-6.5-x86_64-cpython-39/libsbml/_libsbml.cpython-39.so target_dir_path: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/build/lib.dragonfly-6.5-x86_64-cpython-39/libsbml target_lib_path: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/build/lib.dragonfly-6.5-x86_64-cpython-39/libsbml/_libsbml.cpython-39.so suffix: dragonfly-6.5-x86_64-cpython-39 cwd: /construction/biology/py-python-libsbml/python-libsbml-5.20.1 name: _libsbml.cpython-39.so, tmp: build/temp.dragonfly-6.5-x86_64-cpython-39 compiling dependencies cmake /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_dependencies -DCMAKE_BUILD_TYPE=Release -DWITH_STATIC_RUNTIME=ON -DCMAKE_INSTALL_PREFIX=/construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64 -DWITH_BZIP2=ON -DWITH_CHECK=OFF -DWITH_EXPAT=ON -DWITH_XERCES=OFF -DWITH_ICONV=OFF -DWITH_LIBXML=OFF -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/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: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/local/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- 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 ..................... /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64 -- 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 (10.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: WITH_ICONV -- Build files have been written to: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/build_dependencies_dragonfly-6.5-x86_64 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: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/lib/libbz2.a -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/include/bzlib.h -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/include/bzip2/bzlib.h -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/include/expat_config.h -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/lib/libexpat.a -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/include/expat.h -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/include/expat_external.h -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/lib/pkgconfig/expat.pc -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/share/doc/expat/AUTHORS -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/share/doc/expat/changelog -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/lib/cmake/expat-2.4.8/expat-config.cmake -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/lib/cmake/expat-2.4.8/expat-config-version.cmake -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/lib/cmake/expat-2.4.8/expat.cmake -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/lib/cmake/expat-2.4.8/expat-release.cmake -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/lib/libzlib.a -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/include/zconf.h -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/include/zlib.h -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/include/zlib/zconf.h -- Installing: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/include/zlib/zlib.h cmake /construction/biology/py-python-libsbml/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=/construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64 -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/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: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/local/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: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/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 -- Found PythonInterp: /usr/local/bin/python3.9 (found version "3.9.17") -- Found PythonLibs: /usr/local/lib/libpython3.9.so (found version "3.9.17") -- ---------------------------------------------------------------------- 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 'sting.dragonflybsd.org' host type = DragonFly host operating system = DragonFly 6.5 host CPU architecture = x86_64 General build flags: CC = /usr/local/libexec/ccache/cc CXX = /usr/local/libexec/ccache/c++ CPPFLAGS = -DLINUX CFLAGS = -pipe -O2 -fno-strict-aliasing -fno-strict-aliasing -fPIC CXXFLAGS = -pipe -O2 -fno-strict-aliasing -fno-strict-aliasing -fPIC LDFLAGS = XML parser library configuration: XML library = expat CPPFLAGS for XML = 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src/CMakeFiles/sbml-static.dir/sbml/validator/constraints/ValidCnUnitsValue.cpp.o [ 94%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/compress/CompressCommon.cpp.o [ 94%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/compress/InputDecompressor.cpp.o [ 94%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/compress/OutputCompressor.cpp.o [ 94%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/compress/bzfstream.cpp.o [ 94%] Building C object src/CMakeFiles/sbml-static.dir/sbml/compress/zip.c.o [ 94%] Building C object src/CMakeFiles/sbml-static.dir/sbml/compress/unzip.c.o [ 94%] Building C object src/CMakeFiles/sbml-static.dir/sbml/compress/ioapi.c.o In function 'file_build_ioposix', inlined from 'fopen_file_func.constprop' at /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:141:16, inlined from 'fopendisk_file_func' at /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:210:15: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:123:5: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(ioposix->filename, filename, ioposix->filenameLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c: In function 'fopendisk_file_func': /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:121:31: note: length computed here ioposix->filenameLength = strlen(filename) + 1; ^~~~~~~~~~~~~~~~ In function 'file_build_ioposix', inlined from 'fopen_file_func' at /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:141:16: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:123:5: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(ioposix->filename, filename, ioposix->filenameLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c: In function 'fopen_file_func': /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:121:31: note: length computed here ioposix->filenameLength = strlen(filename) + 1; ^~~~~~~~~~~~~~~~ In function 'file_build_ioposix', inlined from 'fopen64_file_func' at /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:160:16: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:123:5: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(ioposix->filename, filename, ioposix->filenameLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c: In function 'fopen64_file_func': /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:121:31: note: length computed here ioposix->filenameLength = strlen(filename) + 1; ^~~~~~~~~~~~~~~~ In function 'file_build_ioposix', inlined from 'fopen64_file_func.constprop' at /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:160:16, inlined from 'fopendisk64_file_func' at /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:185:15: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:123:5: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(ioposix->filename, filename, ioposix->filenameLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c: In function 'fopendisk64_file_func': /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/src/sbml/compress/ioapi.c:121:31: note: length computed here ioposix->filenameLength = strlen(filename) + 1; ^~~~~~~~~~~~~~~~ [ 94%] Building C object src/CMakeFiles/sbml-static.dir/sbml/compress/ioapi_mem.c.o [ 94%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/compress/zfstream.cpp.o [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/compress/zipfstream.cpp.o [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLAttributes.cpp.o [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLBuffer.cpp.o [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLConstructorException.cpp.o [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLError.cpp.o [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLErrorLog.cpp.o [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLLogOverride.cpp.o [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLFileBuffer.cpp.o [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLHandler.cpp.o [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLInputStream.cpp.o [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLMemoryBuffer.cpp.o [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLNamespaces.cpp.o [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLNode.cpp.o [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLOutputStream.cpp.o [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLParser.cpp.o [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLToken.cpp.o [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLTokenizer.cpp.o [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLTriple.cpp.o [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/ExpatAttributes.cpp.o [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/ExpatHandler.cpp.o [ 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 /construction/biology/py-python-libsbml/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' /construction/biology/py-python-libsbml/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' /construction/biology/py-python-libsbml/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 SUCCEEDED 02:08:14 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py39-python-libsbml-5.20.1 ===> 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 ===> Generating temporary packing list Using libSBML from: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source Using VERSION.txt: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/libsbml_source/VERSION.txt Creating: python-libsbml Version is: 5.20.1 building for python: 3.9.17 (main, Jul 29 2023, 01:53:50) [GCC 8.3 [DragonFly] Release/2019-02-22] 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.dragonfly-6.5-x86_64-cpython-39 extension name: _libsbml extension dir: build/lib.dragonfly-6.5-x86_64-cpython-39/libsbml/_libsbml.cpython-39.so target_dir_path: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/build/lib.dragonfly-6.5-x86_64-cpython-39/libsbml target_lib_path: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/build/lib.dragonfly-6.5-x86_64-cpython-39/libsbml/_libsbml.cpython-39.so suffix: dragonfly-6.5-x86_64-cpython-39 cwd: /construction/biology/py-python-libsbml/python-libsbml-5.20.1 name: _libsbml.cpython-39.so, tmp: build/temp.dragonfly-6.5-x86_64-cpython-39 compiling dependencies cmake /construction/biology/py-python-libsbml/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=/construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64 -- Check for working C compiler: /usr/local/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- ---------------------------------------------------------------------- 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 'sting.dragonflybsd.org' host type = DragonFly host operating system = DragonFly 6.5 host CPU architecture = x86_64 General build flags: CC = /usr/local/libexec/ccache/cc CXX = /usr/local/libexec/ccache/c++ CPPFLAGS = -DLINUX CFLAGS = -pipe -O2 -fno-strict-aliasing -fno-strict-aliasing -fPIC CXXFLAGS = -pipe -O2 -fno-strict-aliasing -fno-strict-aliasing -fPIC LDFLAGS = XML parser library configuration: XML library = expat CPPFLAGS for XML = -I/construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/include LIBS for XML = /construction/biology/py-python-libsbml/python-libsbml-5.20.1/install_dependencies_dragonfly-6.5-x86_64/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 (1.3s) -- Generating done (2.9s) -- Build files have been written to: /construction/biology/py-python-libsbml/python-libsbml-5.20.1/build/temp.dragonfly-6.5-x86_64-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 /construction/biology/py-python-libsbml/stage/usr/local/lib/python3.9 creating /construction/biology/py-python-libsbml/stage/usr/local/lib/python3.9/site-packages creating /construction/biology/py-python-libsbml/stage/usr/local/lib/python3.9/site-packages/libsbml copying build/lib.dragonfly-6.5-x86_64-cpython-39/libsbml/_libsbml.cpython-39.so -> /construction/biology/py-python-libsbml/stage/usr/local/lib/python3.9/site-packages/libsbml copying build/lib.dragonfly-6.5-x86_64-cpython-39/libsbml/__init__.py -> /construction/biology/py-python-libsbml/stage/usr/local/lib/python3.9/site-packages/libsbml byte-compiling /construction/biology/py-python-libsbml/stage/usr/local/lib/python3.9/site-packages/libsbml/__init__.py to __init__.cpython-39.pyc writing byte-compilation script '/tmp/tmp22wnisv8.py' /usr/local/bin/python3.9 /tmp/tmp22wnisv8.py removing /tmp/tmp22wnisv8.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 /construction/biology/py-python-libsbml/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 '/construction/biology/py-python-libsbml/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:55 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py39-python-libsbml-5.20.1 file sizes/checksums [8]: 0% file sizes/checksums [8]: 100% Service unavailablepacking files [8]: 0% packing files [8]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:16 TOTAL TIME 02:09:58