[package - 150amd64-default][science/py-pyked] Failed for py311-pyked-0.4.1.16_3 in run-depends
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Date: Sat, 13 Dec 2025 05:10:14 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: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy23/data/150amd64-default/f0beb1ebfa25/logs/py311-pyked-0.4.1.16_3.log
Build URL: https://pkg-status.freebsd.org/beefy23/build.html?mastername=150amd64-default&build=f0beb1ebfa25
Log:
=>> Building science/py-pyked
build started at Sat Dec 13 05:10:09 -00 2025
port directory: /usr/ports/science/py-pyked
package name: py311-pyked-0.4.1.16_3
building for: FreeBSD 150amd64-default-job-18 15.0-RELEASE FreeBSD 15.0-RELEASE amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 962 Sep 30 01:01 /usr/ports/science/py-pyked/Makefile
Ports top last git commit: f0beb1ebfa25330ccd8c6c53bea3e06a7e3cdc6e
Ports top unclean checkout: no
Port dir last git commit: b64b73fd938d5b2788547d16ed6a76493acc9142
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.4-8-ge4f2486b
Host OSVERSION: 1600000
Jail OSVERSION: 1500068
Job Id: 18
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yuri@FreeBSD.org
--End MAINTAINER--
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--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-pyked/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-pyked/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-pyked/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-pyked/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-pyked/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-pyked/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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--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/py311-pyked DOCSDIR=/usr/local/share/doc/py311-pyked EXAMPLESDIR=/usr/local/share/examples/py311-pyked WWWDIR=/usr/local/www/py311-pyked ETCDIR=/usr/local/etc/py311-pyked
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PACKAGES=/packages
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#### ####
# 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*
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---End make.conf---
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file size (512-blocks, -f) unlimited
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max memory size (kbytes, -m) unlimited
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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--
=======================<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-pyked-0.4.1.16_3 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.4.2_1.pkg
[150amd64-default-job-18] Installing pkg-2.4.2_1...
[150amd64-default-job-18] Extracting pkg-2.4.2_1: .......... done
===> py311-pyked-0.4.1.16_3 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py311-pyked-0.4.1.16_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-pyked-0.4.1.16_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-pyked-0.4.1.16_3 for building
=> SHA256 Checksum OK for pr-omethe-us-PyKED-v0.4.1-16-gfcccaf8_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-pyked-0.4.1.16_3 for building
===> Extracting for py311-pyked-0.4.1.16_3
=> SHA256 Checksum OK for pr-omethe-us-PyKED-v0.4.1-16-gfcccaf8_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-pyked-0.4.1.16_3
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-pyked-0.4.1.16_3 depends on package: py311-setuptools>=63.1.0 - not found
===> Installing existing package /packages/All/py311-setuptools-63.1.0_3.pkg
[150amd64-default-job-18] Installing py311-setuptools-63.1.0_3...
[150amd64-default-job-18] `-- Installing python311-3.11.14...
[150amd64-default-job-18] | `-- Installing gettext-runtime-0.23.1...
[150amd64-default-job-18] | | `-- Installing indexinfo-0.3.1_1...
[150amd64-default-job-18] | | `-- Extracting indexinfo-0.3.1_1: .... done
[150amd64-default-job-18] | `-- Extracting gettext-runtime-0.23.1: .......... done
[150amd64-default-job-18] | `-- Installing libffi-3.5.1...
[150amd64-default-job-18] | `-- Extracting libffi-3.5.1: .......... done
[150amd64-default-job-18] | `-- Installing mpdecimal-4.0.1...
[150amd64-default-job-18] | `-- Extracting mpdecimal-4.0.1: .......... done
[150amd64-default-job-18] | `-- Installing readline-8.3.1...
[150amd64-default-job-18] | `-- Extracting readline-8.3.1: .......... done
[150amd64-default-job-18] `-- Extracting python311-3.11.14: .......... done
[150amd64-default-job-18] Extracting py311-setuptools-63.1.0_3: .......... 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-pyked-0.4.1.16_3 depends on package: py311-setuptools>=63.1.0 - found
===> Returning to build of py311-pyked-0.4.1.16_3
===> py311-pyked-0.4.1.16_3 depends on file: /usr/local/bin/python3.11 - found
===========================================================================
=======================<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-pyked-0.4.1.16_3
/usr/local/lib/python3.11/site-packages/setuptools/config/setupcfg.py:463: SetuptoolsDeprecationWarning: The license_file parameter is deprecated, use license_files instead.
warnings.warn(msg, warning_class)
running config
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for py311-pyked-0.4.1.16_3
/usr/local/lib/python3.11/site-packages/setuptools/config/setupcfg.py:463: SetuptoolsDeprecationWarning: The license_file parameter is deprecated, use license_files instead.
warnings.warn(msg, warning_class)
running build
running build_py
creating build
creating build/lib
creating build/lib/pyked
copying pyked/orcid.py -> build/lib/pyked
copying pyked/chemked.py -> build/lib/pyked
copying pyked/__init__.py -> build/lib/pyked
copying pyked/validation.py -> build/lib/pyked
copying pyked/converters.py -> build/lib/pyked
copying pyked/_version.py -> build/lib/pyked
creating build/lib/pyked/tests
copying pyked/tests/__init__.py -> build/lib/pyked/tests
copying pyked/tests/test_validation.py -> build/lib/pyked/tests
copying pyked/tests/test_converters.py -> build/lib/pyked/tests
copying pyked/tests/test_chemked.py -> build/lib/pyked/tests
copying pyked/tests/test_version.py -> build/lib/pyked/tests
running egg_info
creating pyked.egg-info
writing pyked.egg-info/PKG-INFO
writing dependency_links to pyked.egg-info/dependency_links.txt
writing entry points to pyked.egg-info/entry_points.txt
writing requirements to pyked.egg-info/requires.txt
writing top-level names to pyked.egg-info/top_level.txt
writing manifest file 'pyked.egg-info/SOURCES.txt'
reading manifest file 'pyked.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'pyked.egg-info/SOURCES.txt'
/usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyked.schemas' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'pyked.schemas' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'pyked.schemas' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'pyked.schemas' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
creating build/lib/pyked/schemas
copying pyked/schemas/chemked_schema.yaml -> build/lib/pyked/schemas
copying pyked/schemas/composition_schema.yaml -> build/lib/pyked/schemas
copying pyked/schemas/ignition_delay_schema.yaml -> build/lib/pyked/schemas
copying pyked/schemas/value_unit_schema.yaml -> build/lib/pyked/schemas
copying pyked/tests/dataframe_st.csv -> build/lib/pyked/tests
copying pyked/tests/rcm_history.csv -> build/lib/pyked/tests
copying pyked/tests/testfile_bad.yaml -> build/lib/pyked/tests
copying pyked/tests/testfile_many_species.yaml -> build/lib/pyked/tests
copying pyked/tests/testfile_rcm.xml -> build/lib/pyked/tests
copying pyked/tests/testfile_rcm.yaml -> build/lib/pyked/tests
copying pyked/tests/testfile_rcm2.yaml -> build/lib/pyked/tests
copying pyked/tests/testfile_rcm_old.yaml -> build/lib/pyked/tests
copying pyked/tests/testfile_required.yaml -> build/lib/pyked/tests
copying pyked/tests/testfile_st.xml -> build/lib/pyked/tests
copying pyked/tests/testfile_st.yaml -> build/lib/pyked/tests
copying pyked/tests/testfile_st2.yaml -> build/lib/pyked/tests
copying pyked/tests/testfile_st_p5.yaml -> build/lib/pyked/tests
copying pyked/tests/testfile_st_thermo.yaml -> build/lib/pyked/tests
copying pyked/tests/testfile_uncertainty.yaml -> build/lib/pyked/tests
===========================================================================
=======================<phase: run-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-pyked-0.4.1.16_3 depends on package: py311-numpy>=1.16,1<1.27,1 - not found
===> Installing existing package /packages/All/py311-numpy-1.26.4_11,1.pkg
[150amd64-default-job-18] Installing py311-numpy-1.26.4_11,1...
[150amd64-default-job-18] `-- Installing gcc13-13.3.0_3...
[150amd64-default-job-18] | `-- Installing binutils-2.44,1...
[150amd64-default-job-18] | | `-- Installing zstd-1.5.7_1...
[150amd64-default-job-18] | | `-- Extracting zstd-1.5.7_1: .......... done
[150amd64-default-job-18] | `-- Extracting binutils-2.44,1: .......... done
[150amd64-default-job-18] | `-- Installing gmp-6.3.0...
[150amd64-default-job-18] | `-- Extracting gmp-6.3.0: .......... done
[150amd64-default-job-18] | `-- Installing mpc-1.3.1_1...
[150amd64-default-job-18] | | `-- Installing mpfr-4.2.2,1...
[150amd64-default-job-18] | | `-- Extracting mpfr-4.2.2,1: .......... done
[150amd64-default-job-18] | `-- Extracting mpc-1.3.1_1: ......... done
[150amd64-default-job-18] `-- Extracting gcc13-13.3.0_3: .......... done
[150amd64-default-job-18] `-- Installing openblas-0.3.30,2...
[150amd64-default-job-18] `-- Extracting openblas-0.3.30,2: .......... done
[150amd64-default-job-18] `-- Installing suitesparse-umfpack-6.3.7...
[150amd64-default-job-18] | `-- Installing suitesparse-amd-3.3.4...
[150amd64-default-job-18] | | `-- Installing suitesparse-config-7.12.1...
[150amd64-default-job-18] | | `-- Extracting suitesparse-config-7.12.1: .......... done
[150amd64-default-job-18] | `-- Extracting suitesparse-amd-3.3.4: .......... done
[150amd64-default-job-18] | `-- Installing suitesparse-camd-3.3.5...
[150amd64-default-job-18] | `-- Extracting suitesparse-camd-3.3.5: .......... done
[150amd64-default-job-18] | `-- Installing suitesparse-ccolamd-3.3.5...
[150amd64-default-job-18] | `-- Extracting suitesparse-ccolamd-3.3.5: .......... done
[150amd64-default-job-18] | `-- Installing suitesparse-cholmod-5.3.4...
[150amd64-default-job-18] | | `-- Installing suitesparse-colamd-3.3.5...
[150amd64-default-job-18] | | `-- Extracting suitesparse-colamd-3.3.5: .......... done
[150amd64-default-job-18] | `-- Extracting suitesparse-cholmod-5.3.4: .......... done
[150amd64-default-job-18] `-- Extracting suitesparse-umfpack-6.3.7: .......... done
[150amd64-default-job-18] Extracting py311-numpy-1.26.4_11,1: .......... done
=====
Message from gcc13-13.3.0_3:
--
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-pyked-0.4.1.16_3 depends on package: py311-numpy>=1.16,1<1.27,1 - found
===> Returning to build of py311-pyked-0.4.1.16_3
===> py311-pyked-0.4.1.16_3 depends on package: py311-Cerberus>=1.0.0 - not found
===> Installing existing package /packages/All/py311-cerberus-1.3.8_1.pkg
[150amd64-default-job-18] Installing py311-cerberus-1.3.8_1...
[150amd64-default-job-18] Extracting py311-cerberus-1.3.8_1: .......... done
===> py311-pyked-0.4.1.16_3 depends on package: py311-Cerberus>=1.0.0 - not found
*** Error code 1
Stop.
make: stopped making "run-depends" in /usr/ports/science/py-pyked