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Maintainer: j...@freebsd.org Log URL: https://pkg-status.freebsd.org/ampere3/data/141releng-armv7-default/a66c1b68c862/logs/py311-MACS3-3.0.3.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=141releng-armv7-default&build=a66c1b68c862 Log: =>> Building biology/py-macs3 build started at Sat Mar 29 17:23:07 UTC 2025 port directory: /usr/ports/biology/py-macs3 package name: py311-MACS3-3.0.3 building for: FreeBSD 141releng-armv7-default-job-08 14.1-RELEASE-p8 FreeBSD 14.1-RELEASE-p8 1401000 arm maintained by: j...@freebsd.org Makefile datestamp: -rw-r--r-- 1 root wheel 1536 Mar 15 01:05 /usr/ports/biology/py-macs3/Makefile Ports top last git commit: a66c1b68c86 Ports top unclean checkout: no Port dir last git commit: c2d10be9f21 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2-7-gf78625a5 Host OSVERSION: 1500028 Jail OSVERSION: 1401000 Job Id: 08 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1401000 UNAME_v=FreeBSD 14.1-RELEASE-p8 1401000 UNAME_r=14.1-RELEASE-p8 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=3.4.2-7-gf78625a5 MASTERMNT=/usr/local/poudriere/data/.m/141releng-armv7-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/141releng-armv7-default/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=141releng-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/141releng-armv7-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2-7-gf78625a5 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-- j...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-macs3/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-macs3/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-macs3/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-macs3/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-macs3/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-macs3/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-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-macs3/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-macs3/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-macs3/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-macs3/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-macs3/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-macs3/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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-alias ing -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-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.36 DOCSDIR="share/doc/py311-MACS3" EXAMPLESDIR="share/examples/py311-MACS3" DATADIR="share/py311-MACS3" WWWDIR="www/py311-MACS3" ETCDIR="etc/py311-MACS3" --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_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py311-MACS3 DOCSDIR=/usr/local/share/doc/py311-MACS3 EXAMPLESDIR=/usr/local/share/examples/py311-MACS3 WWWDIR=/usr/local/www/py311-MACS3 ETCDIR=/usr/local/etc/py311-MACS3 --End SUB_LIST-- ---Begin make.conf--- # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### 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) 524288 stack size (kbytes, -s) 65536 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 --End resource limits-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-MACS3-3.0.3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.0.6.pkg [141releng-armv7-default-job-08] Installing pkg-2.0.6... [141releng-armv7-default-job-08] Extracting pkg-2.0.6: .......... done ===> py311-MACS3-3.0.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-MACS3-3.0.3 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py311-MACS3-3.0.3 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py311-MACS3-3.0.3 for building => SHA256 Checksum OK for macs3-project-MACS-v3.0.3_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py311-MACS3-3.0.3 for building ===> Extracting for py311-MACS3-3.0.3 => SHA256 Checksum OK for macs3-project-MACS-v3.0.3_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for py311-MACS3-3.0.3 ===> Applying FreeBSD patches for py311-MACS3-3.0.3 from /usr/ports/biology/py-macs3/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-MACS3-3.0.3 depends on package: py311-wheel>0 - not found ===> Installing existing package /packages/All/py311-wheel-0.45.1.pkg [141releng-armv7-default-job-08] Installing py311-wheel-0.45.1... [141releng-armv7-default-job-08] `-- Installing python311-3.11.11... [141releng-armv7-default-job-08] | `-- Installing gettext-runtime-0.23.1... [141releng-armv7-default-job-08] | | `-- Installing indexinfo-0.3.1_1... [141releng-armv7-default-job-08] | | `-- Extracting indexinfo-0.3.1_1: .... done [141releng-armv7-default-job-08] | `-- Extracting gettext-runtime-0.23.1: .......... done [141releng-armv7-default-job-08] | `-- Installing libffi-3.4.6... [141releng-armv7-default-job-08] | `-- Extracting libffi-3.4.6: .......... done [141releng-armv7-default-job-08] | `-- Installing mpdecimal-4.0.0... [141releng-armv7-default-job-08] | `-- Extracting mpdecimal-4.0.0: .......... done [141releng-armv7-default-job-08] | `-- Installing readline-8.2.13_2... [141releng-armv7-default-job-08] | `-- Extracting readline-8.2.13_2: .......... done [141releng-armv7-default-job-08] `-- Extracting python311-3.11.11: .......... done [141releng-armv7-default-job-08] Extracting py311-wheel-0.45.1: .......... done ===== Message from python311-3.11.11: -- 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-MACS3-3.0.3 depends on package: py311-wheel>0 - found ===> Returning to build of py311-MACS3-3.0.3 ===> py311-MACS3-3.0.3 depends on package: simde>0 - not found ===> Installing existing package /packages/All/simde-0.8.2.pkg [141releng-armv7-default-job-08] Installing simde-0.8.2... [141releng-armv7-default-job-08] Extracting simde-0.8.2: .......... done ===> py311-MACS3-3.0.3 depends on package: simde>0 - found ===> Returning to build of py311-MACS3-3.0.3 ===> py311-MACS3-3.0.3 depends on package: py311-cython3>0 - not found ===> Installing existing package /packages/All/py311-cython3-3.0.12.pkg [141releng-armv7-default-job-08] Installing py311-cython3-3.0.12... [141releng-armv7-default-job-08] Extracting py311-cython3-3.0.12: .......... done ===> py311-MACS3-3.0.3 depends on package: py311-cython3>0 - found ===> Returning to build of py311-MACS3-3.0.3 ===> py311-MACS3-3.0.3 depends on package: py311-numpy>=1.16,1<1.27,1 - not found ===> Installing existing package /packages/All/py311-numpy-1.26.4_6,1.pkg [141releng-armv7-default-job-08] Installing py311-numpy-1.26.4_6,1... [141releng-armv7-default-job-08] `-- Installing gcc13-13.3.0_2... [141releng-armv7-default-job-08] | `-- Installing binutils-2.44,1... [141releng-armv7-default-job-08] | | `-- Installing zstd-1.5.7... [141releng-armv7-default-job-08] | | `-- Installing liblz4-1.10.0,1... [141releng-armv7-default-job-08] | | `-- Extracting liblz4-1.10.0,1: .......... done [141releng-armv7-default-job-08] | | `-- Extracting zstd-1.5.7: .......... done [141releng-armv7-default-job-08] | `-- Extracting binutils-2.44,1: .......... done [141releng-armv7-default-job-08] | `-- Installing gmp-6.3.0... [141releng-armv7-default-job-08] | `-- Extracting gmp-6.3.0: .......... done [141releng-armv7-default-job-08] | `-- Installing mpc-1.3.1_1... [141releng-armv7-default-job-08] | | `-- Installing mpfr-4.2.1,1... [141releng-armv7-default-job-08] | | `-- Extracting mpfr-4.2.1,1: .......... done [141releng-armv7-default-job-08] | `-- Extracting mpc-1.3.1_1: ......... done [141releng-armv7-default-job-08] `-- Extracting gcc13-13.3.0_2: .......... done [141releng-armv7-default-job-08] `-- Installing openblas-0.3.29_1,2... [141releng-armv7-default-job-08] `-- Extracting openblas-0.3.29_1,2: .......... done [141releng-armv7-default-job-08] `-- Installing suitesparse-umfpack-6.3.5_1... [141releng-armv7-default-job-08] | `-- Installing suitesparse-amd-3.3.3... [141releng-armv7-default-job-08] | | `-- Installing suitesparse-config-7.8.3_1... [141releng-armv7-default-job-08] | | `-- Extracting suitesparse-config-7.8.3_1: .......... done [141releng-armv7-default-job-08] | `-- Extracting suitesparse-amd-3.3.3: .......... done [141releng-armv7-default-job-08] | `-- Installing suitesparse-camd-3.3.3... [141releng-armv7-default-job-08] | `-- Extracting suitesparse-camd-3.3.3: .......... done [141releng-armv7-default-job-08] | `-- Installing suitesparse-ccolamd-3.3.4... [141releng-armv7-default-job-08] | `-- Extracting suitesparse-ccolamd-3.3.4: .......... done [141releng-armv7-default-job-08] | `-- Installing suitesparse-cholmod-5.3.0_1... [141releng-armv7-default-job-08] | | `-- Installing suitesparse-colamd-3.3.4... [141releng-armv7-default-job-08] | | `-- Extracting suitesparse-colamd-3.3.4: .......... done [141releng-armv7-default-job-08] | `-- Extracting suitesparse-cholmod-5.3.0_1: .......... done [141releng-armv7-default-job-08] `-- Extracting suitesparse-umfpack-6.3.5_1: .......... done [141releng-armv7-default-job-08] Extracting py311-numpy-1.26.4_6,1: .......... done ===== Message from gcc13-13.3.0_2: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> py311-MACS3-3.0.3 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> Returning to build of py311-MACS3-3.0.3 ===> py311-MACS3-3.0.3 depends on package: py311-scipy>1.11.1 - not found ===> Installing existing package /packages/All/py311-scipy-1.11.1_4,1.pkg [141releng-armv7-default-job-08] Installing py311-scipy-1.11.1_4,1... [141releng-armv7-default-job-08] `-- Installing blas-3.12.1... [141releng-armv7-default-job-08] `-- Extracting blas-3.12.1: ........ done [141releng-armv7-default-job-08] Extracting py311-scipy-1.11.1_4,1: .......... done ===> py311-MACS3-3.0.3 depends on package: py311-scipy>1.11.1 - found ===> Returning to build of py311-MACS3-3.0.3 ===> py311-MACS3-3.0.3 depends on package: py311-cykhash>=2.0,<3.0 - not found ===> Installing existing package /packages/All/py311-cykhash-2.0.1_1.pkg [141releng-armv7-default-job-08] Installing py311-cykhash-2.0.1_1... [141releng-armv7-default-job-08] Extracting py311-cykhash-2.0.1_1: .......... done ===> py311-MACS3-3.0.3 depends on package: py311-cykhash>=2.0,<3.0 - found ===> Returning to build of py311-MACS3-3.0.3 ===> py311-MACS3-3.0.3 depends on package: py311-scikit-learn>=1.3 - not found ===> Installing existing package /packages/All/py311-scikit-learn-1.4.0_1.pkg [141releng-armv7-default-job-08] Installing py311-scikit-learn-1.4.0_1... [141releng-armv7-default-job-08] `-- Installing py311-joblib-1.3.2_2... [141releng-armv7-default-job-08] `-- Extracting py311-joblib-1.3.2_2: .......... done [141releng-armv7-default-job-08] `-- Installing py311-threadpoolctl-3.5.0... [141releng-armv7-default-job-08] `-- Extracting py311-threadpoolctl-3.5.0: .......... done [141releng-armv7-default-job-08] Extracting py311-scikit-learn-1.4.0_1: .......... done ===> py311-MACS3-3.0.3 depends on package: py311-scikit-learn>=1.3 - found ===> Returning to build of py311-MACS3-3.0.3 ===> py311-MACS3-3.0.3 depends on package: py311-hmmlearn>=0.3.2 - not found ===> Installing existing package /packages/All/py311-hmmlearn-0.3.3.pkg [141releng-armv7-default-job-08] Installing py311-hmmlearn-0.3.3... [141releng-armv7-default-job-08] Extracting py311-hmmlearn-0.3.3: .......... done ===> py311-MACS3-3.0.3 depends on package: py311-hmmlearn>=0.3.2 - found ===> Returning to build of py311-MACS3-3.0.3 ===> py311-MACS3-3.0.3 depends on file: /usr/local/bin/python3.11 - found ===> py311-MACS3-3.0.3 depends on package: py311-build>=0 - not found ===> Installing existing package /packages/All/py311-build-1.2.2_2.pkg [141releng-armv7-default-job-08] Installing py311-build-1.2.2_2... [141releng-armv7-default-job-08] `-- Installing py311-packaging-24.2... [141releng-armv7-default-job-08] `-- Extracting py311-packaging-24.2: .......... done [141releng-armv7-default-job-08] `-- Installing py311-pyproject-hooks-1.2.0... [141releng-armv7-default-job-08] `-- Extracting py311-pyproject-hooks-1.2.0: .......... done [141releng-armv7-default-job-08] Extracting py311-build-1.2.2_2: .......... done ===> py311-MACS3-3.0.3 depends on package: py311-build>=0 - found ===> Returning to build of py311-MACS3-3.0.3 ===> py311-MACS3-3.0.3 depends on package: py311-installer>=0 - not found ===> Installing existing package /packages/All/py311-installer-0.7.0.pkg [141releng-armv7-default-job-08] Installing py311-installer-0.7.0... [141releng-armv7-default-job-08] Extracting py311-installer-0.7.0: .......... done ===> py311-MACS3-3.0.3 depends on package: py311-installer>=0 - found ===> Returning to build of py311-MACS3-3.0.3 =========================================================================== =======================<phase: lib-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: configure >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py311-MACS3-3.0.3 =========================================================================== =======================<phase: build >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py311-MACS3-3.0.3 * Getting build dependencies for wheel... Traceback (most recent call last): File "/usr/local/lib/python3.11/site-packages/pyproject_hooks/_impl.py", line 402, in _call_hook raise BackendUnavailable( pyproject_hooks._impl.BackendUnavailable: Cannot import 'setuptools.build_meta' ERROR Backend 'setuptools.build_meta' is not available. *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-macs3
