[package - 134amd64-default][biology/py-macs3] Failed for py311-MACS3-3.0.3 in build
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Date: Sun, 16 Mar 2025 17:50:58 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy16/data/134amd64-default/a66c1b68c862/logs/py311-MACS3-3.0.3.log
Build URL: https://pkg-status.freebsd.org/beefy16/build.html?mastername=134amd64-default&build=a66c1b68c862
Log:
=>> Building biology/py-macs3
build started at Sun Mar 16 17:50:16 UTC 2025
port directory: /usr/ports/biology/py-macs3
package name: py311-MACS3-3.0.3
building for: FreeBSD 134amd64-default-job-08 13.4-RELEASE-p4 FreeBSD 13.4-RELEASE-p4 amd64
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1536 Mar 8 01:02 /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: 1304000
Job Id: 08
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POUDRIEREPATH=/usr/local/bin/poudriere
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---Begin Poudriere Port Flags/Env---
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PKGENV=
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MAKE_ARGS= FLAVOR=py311
---End Poudriere Port Flags/Env---
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---End OPTIONS List---
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jwb@FreeBSD.org
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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"
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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=freebsd13 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=13.4 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=freebsd13 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
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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) 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
--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
[134amd64-default-job-08] Installing pkg-2.0.6...
[134amd64-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
[134amd64-default-job-08] Installing py311-wheel-0.45.1...
[134amd64-default-job-08] `-- Installing python311-3.11.11...
[134amd64-default-job-08] | `-- Installing gettext-runtime-0.23.1...
[134amd64-default-job-08] | | `-- Installing indexinfo-0.3.1_1...
[134amd64-default-job-08] | | `-- Extracting indexinfo-0.3.1_1: .... done
[134amd64-default-job-08] | `-- Extracting gettext-runtime-0.23.1: .......... done
[134amd64-default-job-08] | `-- Installing libffi-3.4.6...
[134amd64-default-job-08] | `-- Extracting libffi-3.4.6: .......... done
[134amd64-default-job-08] | `-- Installing mpdecimal-4.0.0...
[134amd64-default-job-08] | `-- Extracting mpdecimal-4.0.0: .......... done
[134amd64-default-job-08] | `-- Installing readline-8.2.13_2...
[134amd64-default-job-08] | `-- Extracting readline-8.2.13_2: .......... done
[134amd64-default-job-08] `-- Extracting python311-3.11.11: .......... done
[134amd64-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
[134amd64-default-job-08] Installing simde-0.8.2...
[134amd64-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
[134amd64-default-job-08] Installing py311-cython3-3.0.12...
[134amd64-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
[134amd64-default-job-08] Installing py311-numpy-1.26.4_6,1...
[134amd64-default-job-08] `-- Installing gcc13-13.3.0_2...
[134amd64-default-job-08] | `-- Installing binutils-2.44,1...
[134amd64-default-job-08] | | `-- Installing zstd-1.5.7...
[134amd64-default-job-08] | | `-- Installing liblz4-1.10.0,1...
[134amd64-default-job-08] | | `-- Extracting liblz4-1.10.0,1: .......... done
[134amd64-default-job-08] | | `-- Extracting zstd-1.5.7: .......... done
[134amd64-default-job-08] | `-- Extracting binutils-2.44,1: .......... done
[134amd64-default-job-08] | `-- Installing gmp-6.3.0...
[134amd64-default-job-08] | `-- Extracting gmp-6.3.0: .......... done
[134amd64-default-job-08] | `-- Installing mpc-1.3.1_1...
[134amd64-default-job-08] | | `-- Installing mpfr-4.2.1,1...
[134amd64-default-job-08] | | `-- Extracting mpfr-4.2.1,1: .......... done
[134amd64-default-job-08] | `-- Extracting mpc-1.3.1_1: ......... done
[134amd64-default-job-08] `-- Extracting gcc13-13.3.0_2: .......... done
[134amd64-default-job-08] `-- Installing openblas-0.3.29_1,2...
[134amd64-default-job-08] `-- Extracting openblas-0.3.29_1,2: .......... done
[134amd64-default-job-08] `-- Installing suitesparse-umfpack-6.3.5_1...
[134amd64-default-job-08] | `-- Installing suitesparse-amd-3.3.3...
[134amd64-default-job-08] | | `-- Installing suitesparse-config-7.8.3_1...
[134amd64-default-job-08] | | `-- Extracting suitesparse-config-7.8.3_1: .......... done
[134amd64-default-job-08] | `-- Extracting suitesparse-amd-3.3.3: .......... done
[134amd64-default-job-08] | `-- Installing suitesparse-camd-3.3.3...
[134amd64-default-job-08] | `-- Extracting suitesparse-camd-3.3.3: .......... done
[134amd64-default-job-08] | `-- Installing suitesparse-ccolamd-3.3.4...
[134amd64-default-job-08] | `-- Extracting suitesparse-ccolamd-3.3.4: .......... done
[134amd64-default-job-08] | `-- Installing suitesparse-cholmod-5.3.0_1...
[134amd64-default-job-08] | | `-- Installing suitesparse-colamd-3.3.4...
[134amd64-default-job-08] | | `-- Extracting suitesparse-colamd-3.3.4: .......... done
[134amd64-default-job-08] | `-- Extracting suitesparse-cholmod-5.3.0_1: .......... done
[134amd64-default-job-08] `-- Extracting suitesparse-umfpack-6.3.5_1: .......... done
[134amd64-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
[134amd64-default-job-08] Installing py311-scipy-1.11.1_4,1...
[134amd64-default-job-08] `-- Installing blas-3.12.1...
[134amd64-default-job-08] `-- Extracting blas-3.12.1: ........ done
[134amd64-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
[134amd64-default-job-08] Installing py311-cykhash-2.0.1_1...
[134amd64-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
[134amd64-default-job-08] Installing py311-scikit-learn-1.4.0_1...
[134amd64-default-job-08] `-- Installing py311-joblib-1.3.2_2...
[134amd64-default-job-08] `-- Extracting py311-joblib-1.3.2_2: .......... done
[134amd64-default-job-08] `-- Installing py311-threadpoolctl-3.5.0...
[134amd64-default-job-08] `-- Extracting py311-threadpoolctl-3.5.0: .......... done
[134amd64-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
[134amd64-default-job-08] Installing py311-hmmlearn-0.3.3...
[134amd64-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
[134amd64-default-job-08] Installing py311-build-1.2.2_2...
[134amd64-default-job-08] `-- Installing py311-packaging-24.2...
[134amd64-default-job-08] `-- Extracting py311-packaging-24.2: .......... done
[134amd64-default-job-08] `-- Installing py311-pyproject-hooks-1.2.0...
[134amd64-default-job-08] `-- Extracting py311-pyproject-hooks-1.2.0: .......... done
[134amd64-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
[134amd64-default-job-08] Installing py311-installer-0.7.0...
[134amd64-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