[package - 135amd64-default][math/py-pyodesys] Failed for py311-pyodesys-0.14.4_2 in run-depends
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Date: Sat, 13 Sep 2025 18:56:45 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/beefy16/data/135amd64-default/56c5cbbc8d99/logs/py311-pyodesys-0.14.4_2.log
Build URL: https://pkg-status.freebsd.org/beefy16/build.html?mastername=135amd64-default&build=56c5cbbc8d99
Log:
=>> Building math/py-pyodesys
build started at Sat Sep 13 18:55:52 UTC 2025
port directory: /usr/ports/math/py-pyodesys
package name: py311-pyodesys-0.14.4_2
building for: FreeBSD 135amd64-default-job-04 13.5-RELEASE-p3 FreeBSD 13.5-RELEASE-p3 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1691 Sep 4 01:03 /usr/ports/math/py-pyodesys/Makefile
Ports top last git commit: 56c5cbbc8d9
Ports top unclean checkout: no
Port dir last git commit: b304d8ab18a
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.3
Host OSVERSION: 1500052
Jail OSVERSION: 1305000
Job Id: 04
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PKGENV=
FLAVOR=py311
MAKE_ARGS= FLAVOR=py311
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===> The following configuration options are available for py311-pyodesys-0.14.4_2:
EXTRAS=on: Install optional dependencies for additional functionality
===> Use 'make config' to modify these settings
---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/math/py-pyodesys/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/math/py-pyodesys/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/math/py-pyodesys/work-py311/.cache HOME=/wrkdirs/usr/ports/math/py-pyodesys/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/math/py-pyodesys/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/math/py-pyodesys/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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--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_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=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/pyodesys" EXAMPLESDIR="share/examples/pyodesys" DATADIR="share/pyodesys" WWWDIR="www/pyodesys" ETCDIR="etc/pyodesys"
--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_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/pyodesys DOCSDIR=/usr/local/share/doc/pyodesys EXAMPLESDIR=/usr/local/share/examples/pyodesys WWWDIR=/usr/local/www/pyodesys ETCDIR=/usr/local/etc/pyodesys
--End SUB_LIST--
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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
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GID=0
UID=0
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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
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-pyodesys-0.14.4_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.3.1.pkg
[135amd64-default-job-04] Installing pkg-2.3.1...
[135amd64-default-job-04] Extracting pkg-2.3.1: .......... done
===> py311-pyodesys-0.14.4_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py311-pyodesys-0.14.4_2
===========================================================================
=======================<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 BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py311-pyodesys-0.14.4_2 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py311-pyodesys-0.14.4_2 for building
=> SHA256 Checksum OK for pyodesys-0.14.4.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 BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py311-pyodesys-0.14.4_2 for building
===> Extracting for py311-pyodesys-0.14.4_2
=> SHA256 Checksum OK for pyodesys-0.14.4.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-pyodesys-0.14.4_2
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-pyodesys-0.14.4_2 depends on executable: Xvfb - not found
===> Installing existing package /packages/All/xorg-vfbserver-21.1.18_1,1.pkg
[135amd64-default-job-04] Installing xorg-vfbserver-21.1.18_1,1...
[135amd64-default-job-04] `-- Installing libXau-1.0.12...
[135amd64-default-job-04] `-- Extracting libXau-1.0.12: .......... done
[135amd64-default-job-04] `-- Installing libXdmcp-1.1.5...
[135amd64-default-job-04] | `-- Installing xorgproto-2024.1...
[135amd64-default-job-04] | `-- Extracting xorgproto-2024.1: .......... done
[135amd64-default-job-04] `-- Extracting libXdmcp-1.1.5: ......... done
[135amd64-default-job-04] `-- Installing libXfont2-2.0.6...
[135amd64-default-job-04] | `-- Installing freetype2-2.13.3...
[135amd64-default-job-04] | | `-- Installing brotli-1.1.0,1...
[135amd64-default-job-04] | | `-- Extracting brotli-1.1.0,1: .......... done
[135amd64-default-job-04] | | `-- Installing png-1.6.49...
[135amd64-default-job-04] | | `-- Extracting png-1.6.49: .......... done
[135amd64-default-job-04] | `-- Extracting freetype2-2.13.3: .......... done
[135amd64-default-job-04] | `-- Installing libfontenc-1.1.8...
[135amd64-default-job-04] | `-- Extracting libfontenc-1.1.8: ......... done
[135amd64-default-job-04] `-- Extracting libXfont2-2.0.6: .......... done
[135amd64-default-job-04] `-- Installing libglvnd-1.7.0...
[135amd64-default-job-04] | `-- Installing libX11-1.8.12,1...
[135amd64-default-job-04] | | `-- Installing libxcb-1.17.0...
[135amd64-default-job-04] | | `-- Extracting libxcb-1.17.0: .......... done
[135amd64-default-job-04] | `-- Extracting libX11-1.8.12,1: .......... done
<snip>
Generating GIO modules cache
==> Running trigger: glib-schemas.ucl
Compiling glib schemas
No schema files found: doing nothing.
==> Running trigger: shared-mime-info.ucl
Building the Shared MIME-Info database cache
=====
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.
=====
Message from libxslt-1.1.43_1:
--
===> NOTICE:
This port is deprecated; you may wish to reconsider installing it:
unmaintained with multiple unfixed security vulnerabilities.
It is scheduled to be removed on or after 2025-09-12.
=====
Message from libinotify-20240724_3:
--
You might want to consider increasing the kern.maxfiles tunable if you plan
to use this library for applications that need to monitor activity of a lot
of files.
=====
Message from libimagequant-4.3.4_5:
--
===> NOTICE:
The libimagequant port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
=====
Message from libraqm-0.10.2:
--
===> NOTICE:
The libraqm port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> py311-pyodesys-0.14.4_2 depends on package: py311-matplotlib>=2.2.5 - found
===> Returning to build of py311-pyodesys-0.14.4_2
===> py311-pyodesys-0.14.4_2 depends on package: py311-numpy>=1.16,1<1.27,1 - found
===> py311-pyodesys-0.14.4_2 depends on package: py311-notebook>=5.7.8 - not found
===> Installing existing package /packages/All/py311-notebook-7.4.5.pkg
[135amd64-default-job-04] Installing py311-notebook-7.4.5...
[135amd64-default-job-04] `-- Installing desktop-file-utils-0.28...
[135amd64-default-job-04] `-- Extracting desktop-file-utils-0.28: .......... done
Building cache database of MIME types
[135amd64-default-job-04] `-- Installing py311-jupyter-server-2.17.0...
[135amd64-default-job-04] | `-- Installing py311-Jinja2-3.1.6...
[135amd64-default-job-04] | | `-- Installing py311-Babel-2.17.0_1...
[135amd64-default-job-04] | | `-- Extracting py311-Babel-2.17.0_1: .......... done
[135amd64-default-job-04] | | `-- Installing py311-markupsafe-3.0.2...
[135amd64-default-job-04] | | `-- Extracting py311-markupsafe-3.0.2: .......... done
[135amd64-default-job-04] | `-- Extracting py311-Jinja2-3.1.6: .......... done
[135amd64-default-job-04] | `-- Installing py311-anyio-4.10.0...
[135amd64-default-job-04] | | `-- Installing py311-idna-3.10...
[135amd64-default-job-04] | | `-- Extracting py311-idna-3.10: .......... done
[135amd64-default-job-04] | | `-- Installing py311-sniffio-1.3.1...
[135amd64-default-job-04] | | `-- Extracting py311-sniffio-1.3.1: .......... done
[135amd64-default-job-04] | | `-- Installing py311-truststore-0.10.4...
[135amd64-default-job-04] | | `-- Extracting py311-truststore-0.10.4: .......... done
[135amd64-default-job-04] | | `-- Installing py311-typing-extensions-4.15.0...
[135amd64-default-job-04] | | `-- Extracting py311-typing-extensions-4.15.0: .......... done
[135amd64-default-job-04] | `-- Extracting py311-anyio-4.10.0: .......... done
[135amd64-default-job-04] | `-- Installing py311-argon2-cffi-21.3.0_2...
[135amd64-default-job-04] | | `-- Installing py311-argon2-cffi-bindings-21.2.0_1...
[135amd64-default-job-04] | | `-- Installing libargon2-20190702_1...
[135amd64-default-job-04] | | `-- Extracting libargon2-20190702_1: .......... done
[135amd64-default-job-04] | | `-- Installing py311-cffi-1.17.1...
[135amd64-default-job-04] | | | `-- Installing py311-pycparser-2.22...
[135amd64-default-job-04] | | | `-- Extracting py311-pycparser-2.22: .......... done
[135amd64-default-job-04] | | `-- Extracting py311-cffi-1.17.1: .......... done
[135amd64-default-job-04] | | `-- Extracting py311-argon2-cffi-bindings-21.2.0_1: .......... done
[135amd64-default-job-04] | `-- Extracting py311-argon2-cffi-21.3.0_2: .......... done
[135amd64-default-job-04] | `-- Installing py311-jupyter-client-8.6.3...
[135amd64-default-job-04] | | `-- Installing py311-jupyter-core-5.8.1...
[135amd64-default-job-04] | | `-- Installing py311-platformdirs-4.4.0...
[135amd64-default-job-04] | | `-- Extracting py311-platformdirs-4.4.0: .......... done
[135amd64-default-job-04] | | `-- Installing py311-traitlets-5.14.3...
[135amd64-default-job-04] | | `-- Extracting py311-traitlets-5.14.3: .......... done
[135amd64-default-job-04] | | `-- Extracting py311-jupyter-core-5.8.1: .......... done
[135amd64-default-job-04] | | `-- Installing py311-pyzmq-27.0.2...
[135amd64-default-job-04] | | `-- Installing libzmq4-4.3.5_2...
[135amd64-default-job-04] | | | `-- Installing libsodium-1.0.19...
[135amd64-default-job-04] | | | `-- Extracting libsodium-1.0.19: .......... done
[135amd64-default-job-04] | | | `-- Installing norm-1.5r6_3...
[135amd64-default-job-04] | | | `-- Extracting norm-1.5r6_3: .... done
[135amd64-default-job-04] | | | `-- Installing openpgm-5.2.122_6...
[135amd64-default-job-04] | | | `-- Extracting openpgm-5.2.122_6: .......... done
[135amd64-default-job-04] | | `-- Extracting libzmq4-4.3.5_2: .......... done
[135amd64-default-job-04] | | `-- Extracting py311-pyzmq-27.0.2: .......... done
[135amd64-default-job-04] | `-- Extracting py311-jupyter-client-8.6.3: .......... done
[135amd64-default-job-04] | `-- Installing py311-jupyter-events-0.12.0_1...
[135amd64-default-job-04] | | `-- Installing py311-fqdn-1.4.0_1...
[135amd64-default-job-04] | | `-- Extracting py311-fqdn-1.4.0_1: .......... done
[135amd64-default-job-04] | | `-- Installing py311-isoduration-20.11.0_1...
[135amd64-default-job-04] | | `-- Installing py311-arrow-1.3.0_1...
[135amd64-default-job-04] | | | `-- Installing py311-types-python-dateutil-2.8.19.14_1...
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[135amd64-default-job-04] | | `-- Extracting py311-arrow-1.3.0_1: .......... done
[135amd64-default-job-04] | | `-- Extracting py311-isoduration-20.11.0_1: .......... done
[135amd64-default-job-04] | | `-- Installing py311-jsonpointer-2.0_1...
[135amd64-default-job-04] | | `-- Extracting py311-jsonpointer-2.0_1: .......... done
[135amd64-default-job-04] | | `-- Installing py311-jsonschema-4.25.1...
[135amd64-default-job-04] | | `-- Installing py311-attrs-25.3.0...
[135amd64-default-job-04] | | `-- Extracting py311-attrs-25.3.0: .......... done
[135amd64-default-job-04] | | `-- Installing py311-jsonschema-specifications-2025.4.1...
[135amd64-default-job-04] | | | `-- Installing py311-referencing-0.36.2...
[135amd64-default-job-04] | | | `-- Installing py311-rpds-py-0.27.1...
[135amd64-default-job-04] | | | `-- Extracting py311-rpds-py-0.27.1: .......... done
[135amd64-default-job-04] | | | `-- Extracting py311-referencing-0.36.2: .......... done
[135amd64-default-job-04] | | `-- Extracting py311-jsonschema-specifications-2025.4.1: .......... done
[135amd64-default-job-04] | | `-- Extracting py311-jsonschema-4.25.1: .......... done
[135amd64-default-job-04] | | `-- Installing py311-python-json-logger-3.3.0...
[135amd64-default-job-04] | | `-- Extracting py311-python-json-logger-3.3.0: .......... done
[135amd64-default-job-04] | | `-- Installing py311-pyyaml-6.0.1_1...
[135amd64-default-job-04] | | `-- Installing libyaml-0.2.5...
[135amd64-default-job-04] | | `-- Extracting libyaml-0.2.5: ......... done
[135amd64-default-job-04] | | `-- Extracting py311-pyyaml-6.0.1_1: .......... done
[135amd64-default-job-04] | | `-- Installing py311-rfc3339-validator-0.1.4_1...
[135amd64-default-job-04] | | `-- Extracting py311-rfc3339-validator-0.1.4_1: .......... done
[135amd64-default-job-04] | | `-- Installing py311-rfc3986-validator-0.1.1_1...
[135amd64-default-job-04] | | `-- Extracting py311-rfc3986-validator-0.1.1_1: .......... done
[135amd64-default-job-04] | | `-- Installing py311-rfc3987-syntax-1.1.0...
[135amd64-default-job-04] | | `-- Installing py311-lark-1.2.2_1...
[135amd64-default-job-04] | | | `-- Installing py311-interegular-0.3.3_1...
[135amd64-default-job-04] | | | `-- Extracting py311-interegular-0.3.3_1: .......... done
[135amd64-default-job-04] | | | `-- Installing py311-regex-2024.11.6...
[135amd64-default-job-04] | | | `-- Extracting py311-regex-2024.11.6: .......... done
[135amd64-default-job-04] | | `-- Extracting py311-lark-1.2.2_1: .......... done
[135amd64-default-job-04] | | `-- Extracting py311-rfc3987-syntax-1.1.0: .......... done
[135amd64-default-job-04] | | `-- Installing py311-uri-template-1.3.0...
[135amd64-default-job-04] | | `-- Extracting py311-uri-template-1.3.0: .......... done
[135amd64-default-job-04] | | `-- Installing py311-webcolors-24.8.0...
[135amd64-default-job-04] | | `-- Extracting py311-webcolors-24.8.0: .......... done
[135amd64-default-job-04] | `-- Extracting py311-jupyter-events-0.12.0_1: .......... done
[135amd64-default-job-04] | `-- Installing py311-jupyter-server-terminals-0.5.3...
[135amd64-default-job-04] | | `-- Installing py311-terminado-0.12.1_1...
[135amd64-default-job-04] | | `-- Installing py311-ptyprocess-0.7.0_1...
[135amd64-default-job-04] | | `-- Extracting py311-ptyprocess-0.7.0_1: .......... done
[135amd64-default-job-04] | | `-- Extracting py311-terminado-0.12.1_1: .......... done
[135amd64-default-job-04] | `-- Extracting py311-jupyter-server-terminals-0.5.3: .......... done
[135amd64-default-job-04] | `-- Installing py311-nbconvert-7.16.6...
[135amd64-default-job-04] | | `-- Installing py311-beautifulsoup-4.13.4_1...
[135amd64-default-job-04] | | `-- Installing py311-html5lib-1.1_1...
[135amd64-default-job-04] | | | `-- Installing py311-webencodings-0.5.1_1...
[135amd64-default-job-04] | | | `-- Extracting py311-webencodings-0.5.1_1: .......... done
[135amd64-default-job-04] | | `-- Extracting py311-html5lib-1.1_1: .......... done
[135amd64-default-job-04] | | `-- Installing py311-lxml5-5.4.0_2...
pkg-static: py311-lxml5-5.4.0_2 conflicts with py311-lxml-6.0.1 (installs files into the same place). Problematic file: /usr/local/lib/python3.11/site-packages/lxml/ElementInclude.py
Failed to install the following 1 package(s): /packages/All/py311-notebook-7.4.5.pkg
==> Running trigger: desktop-file-utils.ucl
Building cache database of MIME types
=====
Message from openpgm-5.2.122_6:
--
===> NOTICE:
The openpgm port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
*** Error code 1
Stop.
make: stopped in /usr/ports/math/py-pyodesys