=>> Building science/py-gemmi build started at Tue Nov 11 21:33:47 EST 2025 port directory: /usr/ports/science/py-gemmi package name: py311-gemmi-0.7.3 building for: FreeBSD pkg.DaveG.ca 15.0-ALPHA3 FreeBSD 15.0-ALPHA3 1500064 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1346 Aug 6 08:11 /usr/ports/science/py-gemmi/Makefile Ports top last git commit: ec159283c191 Ports top unclean checkout: no Port dir last git commit: 1d10f02d6c4d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500064 Job Id: 04 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500064 UNAME_v=FreeBSD 15.0-ALPHA3 1500064 UNAME_r=15.0-ALPHA3 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_c_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py311 MAKE_ARGS= FLAVOR=py311 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-gemmi/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-gemmi/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-gemmi/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-gemmi/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-gemmi/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-gemmi/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-gemmi/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-gemmi/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-gemmi/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-gemmi/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-gemmi/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-gemmi/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/science/py-gemmi/work-py311/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- VER=0.7.3 CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gemmi" EXAMPLESDIR="share/examples/gemmi" DATADIR="share/gemmi" WWWDIR="www/gemmi" ETCDIR="etc/gemmi" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 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 --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-gemmi-0.7.3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> py311-gemmi-0.7.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-gemmi-0.7.3 =========================================================================== =================================================== ===== 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 py311-gemmi-0.7.3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-gemmi-0.7.3 for building => SHA256 Checksum OK for project-gemmi-gemmi-v0.7.3_GH0.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 py311-gemmi-0.7.3 for building ===> Extracting for py311-gemmi-0.7.3 => SHA256 Checksum OK for project-gemmi-gemmi-v0.7.3_GH0.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 py311-gemmi-0.7.3 ===> Applying FreeBSD patches for py311-gemmi-0.7.3 from /usr/ports/science/py-gemmi/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-gemmi-0.7.3 depends on package: py311-pip>0 - not found ===> Installing existing package /packages/All/py311-pip-23.3.2_4.pkg [pkg.DaveG.ca] Installing py311-pip-23.3.2_4... [pkg.DaveG.ca] `-- Installing python311-3.11.14... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.1... [pkg.DaveG.ca] | `-- Extracting readline-8.3.1: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] Extracting py311-pip-23.3.2_4: .......... done ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===== Message from py311-pip-23.3.2_4: -- 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. ===> py311-gemmi-0.7.3 depends on package: py311-pip>0 - found ===> Returning to build of py311-gemmi-0.7.3 ===> py311-gemmi-0.7.3 depends on package: py311-nanobind>0 - not found ===> Installing existing package /packages/All/py311-nanobind-2.4.0.pkg [pkg.DaveG.ca] Installing py311-nanobind-2.4.0... [pkg.DaveG.ca] Extracting py311-nanobind-2.4.0: .......... done ===> py311-gemmi-0.7.3 depends on package: py311-nanobind>0 - found ===> Returning to build of py311-gemmi-0.7.3 ===> py311-gemmi-0.7.3 depends on package: py311-wheel>0 - not found ===> Installing existing package /packages/All/py311-wheel-0.45.1.pkg [pkg.DaveG.ca] Installing py311-wheel-0.45.1... [pkg.DaveG.ca] Extracting py311-wheel-0.45.1: .......... done ===> py311-gemmi-0.7.3 depends on package: py311-wheel>0 - found ===> Returning to build of py311-gemmi-0.7.3 ===> py311-gemmi-0.7.3 depends on package: pybind11>=2.6 - not found ===> Installing existing package /packages/All/pybind11-3.0.1.pkg [pkg.DaveG.ca] Installing pybind11-3.0.1... [pkg.DaveG.ca] Extracting pybind11-3.0.1: .......... done ===> py311-gemmi-0.7.3 depends on package: pybind11>=2.6 - found ===> Returning to build of py311-gemmi-0.7.3 ===> py311-gemmi-0.7.3 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.9.pkg [pkg.DaveG.ca] Installing cmake-core-3.31.9... [pkg.DaveG.ca] `-- Installing expat-2.7.3... [pkg.DaveG.ca] `-- Extracting expat-2.7.3: .......... done [pkg.DaveG.ca] `-- Installing jsoncpp-1.9.6_1... [pkg.DaveG.ca] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg.DaveG.ca] `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | `-- Installing libunistring-1.4.1... [pkg.DaveG.ca] | `-- Extracting libunistring-1.4.1: .......... done [pkg.DaveG.ca] `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] `-- Installing libuv-1.51.0... [pkg.DaveG.ca] `-- Extracting libuv-1.51.0: .......... done [pkg.DaveG.ca] `-- Installing rhash-1.4.4_1... [pkg.DaveG.ca] `-- Extracting rhash-1.4.4_1: .......... done [pkg.DaveG.ca] Extracting cmake-core-3.31.9: .......... done ===> py311-gemmi-0.7.3 depends on file: /usr/local/bin/cmake - found ===> Returning to build of py311-gemmi-0.7.3 ===> py311-gemmi-0.7.3 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.13.1,4.pkg [pkg.DaveG.ca] Installing ninja-1.13.1,4... [pkg.DaveG.ca] Extracting ninja-1.13.1,4: ..... done ===> py311-gemmi-0.7.3 depends on executable: ninja - found ===> Returning to build of py311-gemmi-0.7.3 ===> py311-gemmi-0.7.3 depends on file: /usr/local/bin/python3.11 - found ===> py311-gemmi-0.7.3 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done 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 clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> py311-gemmi-0.7.3 depends on file: /usr/local/bin/ccache - found ===> Returning to build of py311-gemmi-0.7.3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-gemmi-0.7.3 depends on shared library: libgemmi_cpp.so - not found ===> Installing existing package /packages/All/gemmi-0.7.3.pkg [pkg.DaveG.ca] Installing gemmi-0.7.3... [pkg.DaveG.ca] Extracting gemmi-0.7.3: .......... done ===> py311-gemmi-0.7.3 depends on shared library: libgemmi_cpp.so - found (/usr/local/lib/libgemmi_cpp.so) ===> Returning to build of py311-gemmi-0.7.3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py311-gemmi-0.7.3 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/science/py-gemmi/work-py311/.build -- The C compiler identification is Clang 19.1.7 -- The CXX compiler identification is Clang 19.1.7 -- 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 -- Gemmi version 0.7.3 -- Found ZLIB: /usr/lib/libz.so (found version "1.3.1") -- Found gemmi version 0.7.3 -- Build type: Release -- Benchmarks not configured. -- The python module will be built. -- Found Python: /usr/local/bin/python3.11 (found version "3.11.14") found components: Interpreter Development.Module -- Found nanobind 2.4.0: /usr/local/lib/python3.11/site-packages/nanobind -- Configuring done (6.5s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_COLOR_MAKEFILE CMAKE_C_FLAGS_RELEASE CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED Python3_EXECUTABLE Python_ADDITIONAL_VERSIONS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/science/py-gemmi/work-py311/.build =========================================================================== 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