=>> Building biology/py-pyrodigal build started at Tue Dec 16 12:55:17 EST 2025 port directory: /usr/ports/biology/py-pyrodigal package name: py311-pyrodigal-3.6.3 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p1 FreeBSD 14.3-RELEASE-p1 1403000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1109 Jun 29 20:14 /usr/ports/biology/py-pyrodigal/Makefile Ports top last git commit: 10f7dee57a4c Ports top unclean checkout: no Port dir last git commit: 4f0eba1efd73 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 07 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p1 1403000 UNAME_r=14.3-RELEASE-p1 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_14_3_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_14_3_x64-HEAD-ALL/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_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/biology/py-pyrodigal/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pyrodigal/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pyrodigal/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-pyrodigal/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pyrodigal/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-pyrodigal/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-pyrodigal/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pyrodigal/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pyrodigal/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-pyrodigal/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pyrodigal/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-pyrodigal/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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 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=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py311-pyrodigal" EXAMPLESDIR="share/examples/py311-pyrodigal" DATADIR="share/py311-pyrodigal" WWWDIR="www/py311-pyrodigal" ETCDIR="etc/py311-pyrodigal" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 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/py311-pyrodigal DOCSDIR=/usr/local/share/doc/py311-pyrodigal EXAMPLESDIR=/usr/local/share/examples/py311-pyrodigal WWWDIR=/usr/local/www/py311-pyrodigal ETCDIR=/usr/local/etc/py311-pyrodigal --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-pyrodigal-3.6.3 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-pyrodigal-3.6.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-pyrodigal-3.6.3 =========================================================================== =================================================== ===== 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-pyrodigal-3.6.3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-pyrodigal-3.6.3 for building => SHA256 Checksum OK for pyrodigal-3.6.3.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-pyrodigal-3.6.3 for building ===> Extracting for py311-pyrodigal-3.6.3 => SHA256 Checksum OK for pyrodigal-3.6.3.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-pyrodigal-3.6.3 ===> Applying FreeBSD patches for py311-pyrodigal-3.6.3 from /usr/ports/biology/py-pyrodigal/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pyrodigal-3.6.3 depends on package: py311-scikit-build-core>0 - not found ===> Installing existing package /packages/All/py311-scikit-build-core-0.11.6.pkg [pkg.DaveG.ca] Installing py311-scikit-build-core-0.11.6... [pkg.DaveG.ca] `-- Installing py311-packaging-25.0... [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-packaging-25.0: .......... done [pkg.DaveG.ca] `-- Installing py311-pathspec-0.12.1... [pkg.DaveG.ca] `-- Extracting py311-pathspec-0.12.1: .......... done [pkg.DaveG.ca] Extracting py311-scikit-build-core-0.11.6: .......... 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 ===> py311-pyrodigal-3.6.3 depends on package: py311-scikit-build-core>0 - found ===> Returning to build of py311-pyrodigal-3.6.3 ===> py311-pyrodigal-3.6.3 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.10.pkg [pkg.DaveG.ca] Installing cmake-core-3.31.10... [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_2... [pkg.DaveG.ca] `-- Extracting rhash-1.4.4_2: .......... done [pkg.DaveG.ca] Extracting cmake-core-3.31.10: .......... done ===> py311-pyrodigal-3.6.3 depends on file: /usr/local/bin/cmake - found ===> Returning to build of py311-pyrodigal-3.6.3 ===> py311-pyrodigal-3.6.3 depends on package: py311-cython3>=3.2.1 - not found ===> Installing existing package /packages/All/py311-cython3-3.2.1.pkg [pkg.DaveG.ca] Installing py311-cython3-3.2.1... [pkg.DaveG.ca] Extracting py311-cython3-3.2.1: .......... done ===> py311-pyrodigal-3.6.3 depends on package: py311-cython3>=3.2.1 - found ===> Returning to build of py311-pyrodigal-3.6.3 ===> py311-pyrodigal-3.6.3 depends on file: /usr/local/bin/python3.11 - found ===> py311-pyrodigal-3.6.3 depends on package: py311-build>=0 - not found ===> Installing existing package /packages/All/py311-build-1.3.0.pkg [pkg.DaveG.ca] Installing py311-build-1.3.0... [pkg.DaveG.ca] `-- Installing py311-pyproject-hooks-1.2.0... [pkg.DaveG.ca] `-- Extracting py311-pyproject-hooks-1.2.0: .......... done [pkg.DaveG.ca] Extracting py311-build-1.3.0: .......... done ===> py311-pyrodigal-3.6.3 depends on package: py311-build>=0 - found ===> Returning to build of py311-pyrodigal-3.6.3 ===> py311-pyrodigal-3.6.3 depends on package: py311-installer>=0 - not found ===> Installing existing package /packages/All/py311-installer-0.7.0.pkg [pkg.DaveG.ca] Installing py311-installer-0.7.0... [pkg.DaveG.ca] Extracting py311-installer-0.7.0: .......... done ===> py311-pyrodigal-3.6.3 depends on package: py311-installer>=0 - found ===> Returning to build of py311-pyrodigal-3.6.3 ===> py311-pyrodigal-3.6.3 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-pyrodigal-3.6.3 depends on file: /usr/local/bin/ccache - found ===> Returning to build of py311-pyrodigal-3.6.3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py311-pyrodigal-3.6.3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py311-pyrodigal-3.6.3 * Getting build dependencies for wheel... * Building wheel... *** scikit-build-core 0.11.6 using CMake 3.31.10 (wheel) *** Configuring CMake... loading initial cache file build/Release/CMakeInit.txt -- The C 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 -- Try AVX2 C flag = [ ] -- Performing Test HAVE_AVX2 -- Performing Test HAVE_AVX2 - Failed -- Try AVX2 C flag = [-mavx2] -- Performing Test HAVE_AVX2 -- Performing Test HAVE_AVX2 - Success -- Found AVX2: -mavx2 -- Try AVX512 C flag = [ ] -- Performing Test HAVE_AVX512 -- Performing Test HAVE_AVX512 - Failed -- Try AVX512 C flag = [-mavx512f -mavx512bw] -- Performing Test HAVE_AVX512 -- Performing Test HAVE_AVX512 - Success -- Found AVX512: -mavx512f -mavx512bw -- Try NEON C flag = [ ] -- Performing Test HAVE_NEON -- Performing Test HAVE_NEON - Failed -- Try NEON C flag = [-mfpu=neon] -- Performing Test HAVE_NEON -- Performing Test HAVE_NEON - Failed -- Try NEON C flag = [-mfpu=neon -mfloat-abi=softfp] -- Performing Test HAVE_NEON -- Performing Test HAVE_NEON - Failed -- Could NOT find NEON (missing: NEON_C_FLAGS) -- Try SSE2 C flag = [ ] -- Performing Test HAVE_SSE2 -- Performing Test HAVE_SSE2 - Success -- Found SSE2: -- Found Python: /usr/local/bin/python3.11 (found version "3.11.14") found components: Interpreter Development.Module -- Looking for PyInterpreterState_GetID -- Looking for PyInterpreterState_GetID - not found -- Configuring done (4.0s) -- Generating done (0.0s) -- Build files have been written to: /wrkdirs/usr/ports/biology/py-pyrodigal/work-py311/pyrodigal-3.6.3/build/Release *** Building project with Unix Makefiles... 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Building C object src/pyrodigal/impl/CMakeFiles/pyrodigal.impl.avx512.dir/cmake_pch.h.pch [ 99%] Building C object src/pyrodigal/impl/CMakeFiles/pyrodigal.impl.avx512.dir/avx512.c.o [100%] Linking C shared module avx512.cpython-311.so [100%] Built target pyrodigal.impl.avx512 *** Installing project into wheel... -- Install configuration: "Release" -- Installing: /tmp/tmpyhpzsmzg/wheel/platlib/pyrodigal/impl/generic.cpython-311.so -- Installing: /tmp/tmpyhpzsmzg/wheel/platlib/pyrodigal/impl/sse2.cpython-311.so -- Installing: /tmp/tmpyhpzsmzg/wheel/platlib/pyrodigal/impl/avx2.cpython-311.so -- Installing: /tmp/tmpyhpzsmzg/wheel/platlib/pyrodigal/impl/avx512.cpython-311.so -- Installing: /tmp/tmpyhpzsmzg/wheel/platlib/pyrodigal/lib.cpython-311.so *** Making wheel... *** Created pyrodigal-3.6.3-cp311-cp311-freebsd_14_3_release_p1_amd64.whl Successfully built pyrodigal-3.6.3-cp311-cp311-freebsd_14_3_release_p1_amd64.whl =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pyrodigal-3.6.3 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py311-pyrodigal-3.6.3 ===> Generating temporary packing list ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/pyrodigal --> bin/pyrodigal-3.11 Link: @bin/pyrodigal --> bin/pyrodigal-3.11 ====> 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=2025-12-16T17:55:17+0000' 'PKG_NOTE_ports_top_git_hash=10f7dee57a4c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=4f0eba1efd73' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for py311-pyrodigal-3.6.3 ===> Building py311-pyrodigal-3.6.3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-pyrodigal-3.6.3 build of biology/py-pyrodigal@py311 | py311-pyrodigal-3.6.3 ended at Tue Dec 16 12:57:35 EST 2025 build time: 00:02:18