------------------------------------------------------------------------------- -- 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/science/py-gemmi XDG_CONFIG_HOME=/construction/science/py-gemmi XDG_CACHE_HOME=/construction/science/py-gemmi/.cache HOME=/construction/science/py-gemmi TMPDIR="/tmp" PATH=/construction/science/py-gemmi/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/py-gemmi/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/science/py-gemmi XDG_CONFIG_HOME=/construction/science/py-gemmi XDG_CACHE_HOME=/construction/science/py-gemmi/.cache HOME=/construction/science/py-gemmi TMPDIR="/tmp" PATH=/construction/science/py-gemmi/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/py-gemmi/.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 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="gcc" CFLAGS="-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="g++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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/science/py-gemmi/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- VER=0.6.2 CMAKE_BUILD_TYPE="release" 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/gemmi" EXAMPLESDIR="share/examples/gemmi" DATADIR="share/gemmi" WWWDIR="www/gemmi" ETCDIR="etc/gemmi" 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/gemmi DOCSDIR=/usr/local/share/doc/gemmi EXAMPLESDIR=/usr/local/share/examples/gemmi WWWDIR=/usr/local/www/gemmi ETCDIR=/usr/local/etc/gemmi 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/indexinfo-0.3.1.pkg Installing /packages/All/libffi-3.4.4.pkg Installing /packages/All/expat-2.5.0.pkg Installing /packages/All/mpdecimal-2.5.1.pkg Installing /packages/All/ncurses-6.4.pkg ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/readline-8.2.1.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/openssl-1.1.1u,1.pkg Installing /packages/All/python39-3.9.17.pkg ===== 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 Installing /packages/All/py39-pip-23.1.2.pkg ===== Message from py39-pip-23.1.2: -- pip MUST ONLY be used: * With the --user flag, OR * To install or manage Python packages in virtual environments Failure to follow this warning can and will result in an inconsistent system-wide Python environment (LOCALBASE/lib/pythonX.Y/site-packages) and cause errors. Avoid using pip as root unless you know what you're doing. Installing /packages/All/py39-pybind11-2.10.4.pkg Installing /packages/All/py39-wheel-0.40.0_1.pkg Installing /packages/All/pybind11-2.10.4.pkg Installing /packages/All/libuv-1.46.0.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/cmake-core-3.26.1_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. Installing /packages/All/gemmi-0.6.2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py39-gemmi-0.6.2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py39-gemmi-0.6.2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-gemmi-0.6.2 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py39-gemmi-0.6.2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-gemmi-0.6.2 for building => SHA256 Checksum OK for project-gemmi-gemmi-v0.6.2_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py39-gemmi-0.6.2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-gemmi-0.6.2 for building ===> Extracting for py39-gemmi-0.6.2 => SHA256 Checksum OK for project-gemmi-gemmi-v0.6.2_GH0.tar.gz. Extracted Memory Use: 6.47M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py39-gemmi-0.6.2 ===> Applying ports patches for py39-gemmi-0.6.2 from /xports/science/py-gemmi/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py39-gemmi-0.6.2 depends on package: py39-pip>0 - found ===> py39-gemmi-0.6.2 depends on package: py39-pybind11>0 - found ===> py39-gemmi-0.6.2 depends on package: py39-wheel>0 - found ===> py39-gemmi-0.6.2 depends on package: pybind11>=2.6 - found ===> py39-gemmi-0.6.2 depends on file: /usr/local/bin/cmake - found ===> py39-gemmi-0.6.2 depends on file: /usr/local/bin/python3.9 - found ===> py39-gemmi-0.6.2 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> py39-gemmi-0.6.2 depends on shared library: libgemmi_cpp.so - found (/usr/local/lib/libgemmi_cpp.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py39-gemmi-0.6.2 depends on package: py39-pip>0 - found ===> py39-gemmi-0.6.2 depends on package: py39-pybind11>0 - found ===> py39-gemmi-0.6.2 depends on package: py39-wheel>0 - found ===> py39-gemmi-0.6.2 depends on package: pybind11>=2.6 - found ===> py39-gemmi-0.6.2 depends on file: /usr/local/bin/cmake - found ===> py39-gemmi-0.6.2 depends on file: /usr/local/bin/python3.9 - found ===> py39-gemmi-0.6.2 depends on file: /usr/local/bin/ccache - found ===> py39-gemmi-0.6.2 depends on shared library: libgemmi_cpp.so - found (/usr/local/lib/libgemmi_cpp.so) ===> Configuring for py39-gemmi-0.6.2 ===> Performing out-of-source build /bin/mkdir -p /construction/science/py-gemmi/.build -- 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/gcc - 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/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Gemmi version 0.6.2 -- Interprocedural optimization not supported: -- Compiling with C++ standard: 20 -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") -- Benchmarks not configured. -- Found gemmi version 0.6.2 -- The python module will be built. -- Found Python: /usr/local/bin/python3.9 (found version "3.9.17") found components: Interpreter Development Development.Module Development.Embed -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/local/include (found version "2.10.4") -- Found pybind11 2.10.4: /usr/local/include;/usr/local/include/python3.9 -- Configuring done (7.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_C_FLAGS_RELEASE CMAKE_SHARED_LINKER_FLAGS FETCHCONTENT_FULLY_DISCONNECTED Python_ADDITIONAL_VERSIONS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /construction/science/py-gemmi/.build SUCCEEDED 00:00:09 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py39-gemmi-0.6.2 /usr/local/bin/cmake -S/construction/science/py-gemmi/gemmi-0.6.2 -B/construction/science/py-gemmi/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/science/py-gemmi/.build/CMakeFiles /construction/science/py-gemmi/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- CMakeFiles/options.dir/all --- --- CMakeFiles/gemmi_py.dir/all --- --- CMakeFiles/options.dir/all --- /usr/bin/make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend --- CMakeFiles/gemmi_py.dir/all --- /usr/bin/make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/depend --- CMakeFiles/options.dir/all --- --- CMakeFiles/options.dir/depend --- cd /construction/science/py-gemmi/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/py-gemmi/gemmi-0.6.2 /construction/science/py-gemmi/gemmi-0.6.2 /construction/science/py-gemmi/.build /construction/science/py-gemmi/.build /construction/science/py-gemmi/.build/CMakeFiles/options.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build --- CMakeFiles/options.dir/prog/options.cpp.o --- [ 0%] Building CXX object CMakeFiles/options.dir/prog/options.cpp.o /usr/local/libexec/ccache/g++ -I/construction/science/py-gemmi/gemmi-0.6.2/include -I/construction/science/py-gemmi/gemmi-0.6.2/third_party -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++2a -fvisibility-inlines-hidden -MD -MT CMakeFiles/options.dir/prog/options.cpp.o -MF CMakeFiles/options.dir/prog/options.cpp.o.d -o CMakeFiles/options.dir/prog/options.cpp.o -c /construction/science/py-gemmi/gemmi-0.6.2/prog/options.cpp --- CMakeFiles/gemmi_py.dir/all --- --- CMakeFiles/gemmi_py.dir/depend --- cd /construction/science/py-gemmi/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/py-gemmi/gemmi-0.6.2 /construction/science/py-gemmi/gemmi-0.6.2 /construction/science/py-gemmi/.build /construction/science/py-gemmi/.build /construction/science/py-gemmi/.build/CMakeFiles/gemmi_py.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/build --- CMakeFiles/gemmi_py.dir/python/mol.cpp.o --- --- CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o --- --- CMakeFiles/gemmi_py.dir/python/align.cpp.o --- --- CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o --- --- CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o --- --- CMakeFiles/gemmi_py.dir/python/cif.cpp.o --- --- CMakeFiles/gemmi_py.dir/python/custom.cpp.o --- --- CMakeFiles/gemmi_py.dir/python/elem.cpp.o --- --- CMakeFiles/gemmi_py.dir/python/grid.cpp.o --- --- CMakeFiles/gemmi_py.dir/python/hkl.cpp.o --- --- CMakeFiles/gemmi_py.dir/python/meta.cpp.o --- --- CMakeFiles/gemmi_py.dir/python/monlib.cpp.o --- --- CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o --- [ 12%] Building CXX object CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o --- CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o --- [ 12%] Building CXX object CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o /usr/local/libexec/ccache/g++ -DGEMMI_SHARED -Dgemmi_py_EXPORTS -I/construction/science/py-gemmi/gemmi-0.6.2/include -I/construction/science/py-gemmi/gemmi-0.6.2/third_party -isystem /usr/local/include/python3.9 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++2a -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -MF CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -c /construction/science/py-gemmi/gemmi-0.6.2/python/ccp4.cpp --- CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o --- /usr/local/libexec/ccache/g++ -DGEMMI_SHARED -Dgemmi_py_EXPORTS -I/construction/science/py-gemmi/gemmi-0.6.2/include -I/construction/science/py-gemmi/gemmi-0.6.2/third_party -isystem /usr/local/include/python3.9 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++2a -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o -MF CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o -c /construction/science/py-gemmi/gemmi-0.6.2/python/gemmi.cpp --- CMakeFiles/gemmi_py.dir/python/align.cpp.o --- [ 25%] Building CXX object CMakeFiles/gemmi_py.dir/python/align.cpp.o /usr/local/libexec/ccache/g++ -DGEMMI_SHARED -Dgemmi_py_EXPORTS -I/construction/science/py-gemmi/gemmi-0.6.2/include -I/construction/science/py-gemmi/gemmi-0.6.2/third_party -isystem /usr/local/include/python3.9 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++2a -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/align.cpp.o -MF CMakeFiles/gemmi_py.dir/python/align.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/align.cpp.o -c /construction/science/py-gemmi/gemmi-0.6.2/python/align.cpp --- CMakeFiles/gemmi_py.dir/python/custom.cpp.o --- [ 18%] Building CXX object CMakeFiles/gemmi_py.dir/python/custom.cpp.o /usr/local/libexec/ccache/g++ -DGEMMI_SHARED -Dgemmi_py_EXPORTS -I/construction/science/py-gemmi/gemmi-0.6.2/include -I/construction/science/py-gemmi/gemmi-0.6.2/third_party -isystem /usr/local/include/python3.9 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++2a -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/custom.cpp.o -MF CMakeFiles/gemmi_py.dir/python/custom.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/custom.cpp.o -c /construction/science/py-gemmi/gemmi-0.6.2/python/custom.cpp --- CMakeFiles/gemmi_py.dir/python/hkl.cpp.o --- [ 31%] Building CXX object CMakeFiles/gemmi_py.dir/python/hkl.cpp.o /usr/local/libexec/ccache/g++ -DGEMMI_SHARED -Dgemmi_py_EXPORTS -I/construction/science/py-gemmi/gemmi-0.6.2/include -I/construction/science/py-gemmi/gemmi-0.6.2/third_party -isystem /usr/local/include/python3.9 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++2a -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -MF CMakeFiles/gemmi_py.dir/python/hkl.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -c /construction/science/py-gemmi/gemmi-0.6.2/python/hkl.cpp --- CMakeFiles/gemmi_py.dir/python/cif.cpp.o --- [ 31%] Building CXX object CMakeFiles/gemmi_py.dir/python/cif.cpp.o --- CMakeFiles/gemmi_py.dir/python/elem.cpp.o --- [ 25%] Building CXX object CMakeFiles/gemmi_py.dir/python/elem.cpp.o --- CMakeFiles/gemmi_py.dir/python/cif.cpp.o --- /usr/local/libexec/ccache/g++ -DGEMMI_SHARED -Dgemmi_py_EXPORTS -I/construction/science/py-gemmi/gemmi-0.6.2/include -I/construction/science/py-gemmi/gemmi-0.6.2/third_party -isystem /usr/local/include/python3.9 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 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/usr/include/c++/8.0/bits/stl_heap.h:214:5: note: the ABI of passing structure with complex float member has changed in GCC 4.4 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^ /usr/include/c++/8.0/bits/stl_heap.h: In function '_ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPN5gemmi8HklValueISt7complexIfEEESt6vectorIS6_SaIS6_EEEElNS0_5__ops15_Iter_less_iterEEvT_SE_T0_T1_.isra.2644': /usr/include/c++/8.0/bits/stl_heap.h:342:22: note: the ABI of passing structure with complex float member has changed in GCC 4.4 std::__adjust_heap(__first, __parent, __len, _GLIBCXX_MOVE(__value), ^ Installing the project stripped... /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /construction/science/py-gemmi/stage/usr/local/lib/python3.9/site-packages/gemmi.cpython-39.so running install_egg_info /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 egg_info creating gemmi.egg-info writing gemmi.egg-info/PKG-INFO writing dependency_links to gemmi.egg-info/dependency_links.txt writing top-level names to gemmi.egg-info/top_level.txt writing manifest file 'gemmi.egg-info/SOURCES.txt' reading manifest file 'gemmi.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.txt' writing manifest file 'gemmi.egg-info/SOURCES.txt' Copying gemmi.egg-info to /construction/science/py-gemmi/stage/usr/local/lib/python3.9/site-packages/gemmi-0.6.2-py3.9.egg-info ====> 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 00:06:07 ------------------------------------------------------------------------------- -- 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 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py39-gemmi-0.6.2 file sizes/checksums [6]: 0% file sizes/checksums [6]: 100% Service unavailablepacking files [6]: 0% packing files [6]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:03 TOTAL TIME 00:18:45