[package - 142i386-default][science/py-pymatgen] Failed for py311-pymatgen-2025.6.14_1 in run-depends
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Date: Sat, 13 Sep 2025 02:25:22 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/beefy21/data/142i386-default/56c5cbbc8d99/logs/py311-pymatgen-2025.6.14_1.log
Build URL: https://pkg-status.freebsd.org/beefy21/build.html?mastername=142i386-default&build=56c5cbbc8d99
Log:
=>> Building science/py-pymatgen
build started at Sat Sep 13 02:24:39 UTC 2025
port directory: /usr/ports/science/py-pymatgen
package name: py311-pymatgen-2025.6.14_1
building for: FreeBSD 142i386-default-job-08 14.2-RELEASE-p5 FreeBSD 14.2-RELEASE-p5 i386
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 3139 Sep 2 01:01 /usr/ports/science/py-pymatgen/Makefile
Ports top last git commit: 56c5cbbc8d
Ports top unclean checkout: no
Port dir last git commit: b304d8ab18
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.3
Host OSVERSION: 1500052
Jail OSVERSION: 1402000
Job Id: 08
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yuri@FreeBSD.org
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PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-pymatgen/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-pymatgen/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-pymatgen/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-pymatgen/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-pymatgen/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-pymatgen/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--
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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-pymatgen DOCSDIR=/usr/local/share/doc/py311-pymatgen EXAMPLESDIR=/usr/local/share/examples/py311-pymatgen WWWDIR=/usr/local/www/py311-pymatgen ETCDIR=/usr/local/etc/py311-pymatgen
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#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
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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 MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-pymatgen-2025.6.14_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.3.1.pkg
[142i386-default-job-08] Installing pkg-2.3.1...
[142i386-default-job-08] Extracting pkg-2.3.1: .......... done
===> py311-pymatgen-2025.6.14_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py311-pymatgen-2025.6.14_1
===========================================================================
=======================<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 MIT accepted by the user
===> Fetching all distfiles required by py311-pymatgen-2025.6.14_1 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by py311-pymatgen-2025.6.14_1 for building
=> SHA256 Checksum OK for materialsproject-pymatgen-v2025.6.14_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 MIT accepted by the user
===> Fetching all distfiles required by py311-pymatgen-2025.6.14_1 for building
===> Extracting for py311-pymatgen-2025.6.14_1
=> SHA256 Checksum OK for materialsproject-pymatgen-v2025.6.14_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-pymatgen-2025.6.14_1
===> Applying FreeBSD patches for py311-pymatgen-2025.6.14_1 from /usr/ports/science/py-pymatgen/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-pymatgen-2025.6.14_1 depends on package: py311-setuptools>0 - not found
===> Installing existing package /packages/All/py311-setuptools-63.1.0_3.pkg
[142i386-default-job-08] Installing py311-setuptools-63.1.0_3...
[142i386-default-job-08] `-- Installing python311-3.11.13_1...
[142i386-default-job-08] | `-- Installing gettext-runtime-0.23.1...
[142i386-default-job-08] | | `-- Installing indexinfo-0.3.1_1...
[142i386-default-job-08] | | `-- Extracting indexinfo-0.3.1_1: .... done
[142i386-default-job-08] | `-- Extracting gettext-runtime-0.23.1: .......... done
[142i386-default-job-08] | `-- Installing libffi-3.5.1...
[142i386-default-job-08] | `-- Extracting libffi-3.5.1: .......... done
[142i386-default-job-08] | `-- Installing mpdecimal-4.0.1...
[142i386-default-job-08] | `-- Extracting mpdecimal-4.0.1: .......... done
[142i386-default-job-08] | `-- Installing readline-8.2.13_2...
[142i386-default-job-08] | `-- Extracting readline-8.2.13_2: .......... done
[142i386-default-job-08] `-- Extracting python311-3.11.13_1: .......... done
[142i386-default-job-08] Extracting py311-setuptools-63.1.0_3: .......... done
=====
Message from python311-3.11.13_1:
<snip>
[142i386-default-job-08] | | | `-- Installing pinentry-1.3.2...
[142i386-default-job-08] | | | | `-- Installing pinentry-curses-1.3.2...
[142i386-default-job-08] | | | | `-- Extracting pinentry-curses-1.3.2: .... done
[142i386-default-job-08] | | | `-- Extracting pinentry-1.3.2: ..... done
[142i386-default-job-08] | | | `-- Extracting gnupg-2.4.8: .......... done
[142i386-default-job-08] | | `-- Extracting gpgme-2.0.0: .......... done
[142i386-default-job-08] | | `-- Installing gpgmepp-2.0.0...
[142i386-default-job-08] | | `-- Extracting gpgmepp-2.0.0: .......... done
[142i386-default-job-08] | | `-- Installing nspr-4.37...
[142i386-default-job-08] | | `-- Extracting nspr-4.37: .......... done
[142i386-default-job-08] | | `-- Installing nss-3.116...
[142i386-default-job-08] | | `-- Extracting nss-3.116: .......... done
[142i386-default-job-08] | | `-- Installing poppler-data-0.4.12...
[142i386-default-job-08] | | `-- Extracting poppler-data-0.4.12: .......... done
[142i386-default-job-08] | | `-- Extracting poppler-25.04.0_2: .......... done
[142i386-default-job-08] | | `-- Installing postgresql17-client-17.6_1...
[142i386-default-job-08] | | `-- Extracting postgresql17-client-17.6_1: .......... done
[142i386-default-job-08] | | `-- Installing sfcgal-2.2.0...
[142i386-default-job-08] | | `-- Extracting sfcgal-2.2.0: .......... done
[142i386-default-job-08] | | `-- Installing spatialite-5.1.0_4...
[142i386-default-job-08] | | `-- Installing librttopo-1.1.0...
[142i386-default-job-08] | | `-- Extracting librttopo-1.1.0: .......... done
[142i386-default-job-08] | | `-- Extracting spatialite-5.1.0_4: .......... done
[142i386-default-job-08] | | `-- Installing xerces-c3-3.3.0...
[142i386-default-job-08] | | `-- Extracting xerces-c3-3.3.0: .......... done
[142i386-default-job-08] | `-- Extracting gdal-3.11.3_4: .......... done
[142i386-default-job-08] `-- Extracting py311-gdal-3.11.3: .......... done
[142i386-default-job-08] `-- Installing py311-pydot-4.0.1...
[142i386-default-job-08] | `-- Installing graphviz-12.2.1_2...
[142i386-default-job-08] | | `-- Installing cairo-1.18.2,3...
[142i386-default-job-08] | | `-- Installing lzo2-2.10_1...
[142i386-default-job-08] | | `-- Extracting lzo2-2.10_1: .......... done
[142i386-default-job-08] | | `-- Installing pixman-0.46.2...
[142i386-default-job-08] | | `-- Extracting pixman-0.46.2: ......... done
[142i386-default-job-08] | | `-- Extracting cairo-1.18.2,3: .......... done
[142i386-default-job-08] | | `-- Installing libICE-1.1.2,1...
[142i386-default-job-08] | | `-- Extracting libICE-1.1.2,1: .......... done
[142i386-default-job-08] | | `-- Installing libSM-1.2.6,1...
[142i386-default-job-08] | | `-- Extracting libSM-1.2.6,1: .......... done
[142i386-default-job-08] | | `-- Installing libXaw-1.0.16,2...
[142i386-default-job-08] | | `-- Installing libXmu-1.1.4,1...
[142i386-default-job-08] | | | `-- Installing libXt-1.3.0,1...
[142i386-default-job-08] | | | `-- Extracting libXt-1.3.0,1: .......... done
[142i386-default-job-08] | | `-- Extracting libXmu-1.1.4,1: .......... done
[142i386-default-job-08] | | `-- Installing libXpm-3.5.17_1...
[142i386-default-job-08] | | `-- Extracting libXpm-3.5.17_1: .......... done
[142i386-default-job-08] | | `-- Extracting libXaw-1.0.16,2: .......... done
[142i386-default-job-08] | | `-- Installing libgd-2.3.3_13,1...
[142i386-default-job-08] | | `-- Extracting libgd-2.3.3_13,1: .......... done
[142i386-default-job-08] | | `-- Installing libltdl-2.5.4...
[142i386-default-job-08] | | `-- Extracting libltdl-2.5.4: .......... done
[142i386-default-job-08] | | `-- Installing pango-1.56.1...
[142i386-default-job-08] | | `-- Installing libthai-0.1.29_1...
[142i386-default-job-08] | | | `-- Installing libdatrie-0.2.13_2...
[142i386-default-job-08] | | | `-- Extracting libdatrie-0.2.13_2: .......... done
[142i386-default-job-08] | | `-- Extracting libthai-0.1.29_1: .......... done
[142i386-default-job-08] | | `-- Extracting pango-1.56.1: .......... done
[142i386-default-job-08] | `-- Extracting graphviz-12.2.1_2: .......... done
[142i386-default-job-08] `-- Extracting py311-pydot-4.0.1: .......... done
[142i386-default-job-08] `-- Installing py311-pygraphviz-1.6_1...
[142i386-default-job-08] `-- Extracting py311-pygraphviz-1.6_1: .......... done
[142i386-default-job-08] `-- Installing py311-pyyaml-6.0.1_1...
[142i386-default-job-08] | `-- Installing libyaml-0.2.5...
[142i386-default-job-08] | `-- Extracting libyaml-0.2.5: ......... done
[142i386-default-job-08] `-- Extracting py311-pyyaml-6.0.1_1: .......... done
[142i386-default-job-08] `-- Installing py311-scikit-sparse-0.4.16_1...
[142i386-default-job-08] | `-- Installing py311-scipy-1.11.1_4,1...
[142i386-default-job-08] | | `-- Installing blas-3.12.1...
[142i386-default-job-08] | | `-- Extracting blas-3.12.1: ........ done
[142i386-default-job-08] | `-- Extracting py311-scipy-1.11.1_4,1: .......... done
[142i386-default-job-08] `-- Extracting py311-scikit-sparse-0.4.16_1: .......... done
[142i386-default-job-08] Extracting py311-networkx-3.5_3,2: .......... done
=====
Message from boost-libs-1.88.0_2:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
=====
Message from postgresql17-client-17.6_1:
--
The PostgreSQL port has a collection of "side orders":
postgresql-docs
For all of the html documentation
p5-Pg
A perl5 API for client access to PostgreSQL databases.
postgresql-tcltk
If you want tcl/tk client support.
postgresql-jdbc
For Java JDBC support.
postgresql-odbc
For client access from unix applications using ODBC as access
method. Not needed to access unix PostgreSQL servers from Win32
using ODBC. See below.
ruby-postgres, py-psycopg
For client access to PostgreSQL databases using the ruby & python
languages.
postgresql-plperl, postgresql-pltcl & postgresql-plruby
For using perl5, tcl & ruby as procedural languages.
postgresql-contrib
Lots of contributed utilities, postgresql functions and
datatypes. There you find pg_standby, pgcrypto and many other cool
things.
etc...
===> py311-pymatgen-2025.6.14_1 depends on package: py311-networkx>=2.7 - found
===> Returning to build of py311-pymatgen-2025.6.14_1
===> py311-pymatgen-2025.6.14_1 depends on package: py311-numpy>=1.16,1<1.27,1 - found
===> py311-pymatgen-2025.6.14_1 depends on package: py311-orjson>=3.10 - found
===> py311-pymatgen-2025.6.14_1 depends on package: py311-palettable>=3.3.3 - not found
===> Installing existing package /packages/All/py311-palettable-3.3.3.pkg
[142i386-default-job-08] Installing py311-palettable-3.3.3...
[142i386-default-job-08] Extracting py311-palettable-3.3.3: .......... done
===> py311-pymatgen-2025.6.14_1 depends on package: py311-palettable>=3.3.3 - found
===> Returning to build of py311-pymatgen-2025.6.14_1
===> py311-pymatgen-2025.6.14_1 depends on package: py311-pandas>=2 - found
===> py311-pymatgen-2025.6.14_1 depends on package: py311-plotly>=5.0.0 - not found
===> Installing existing package /packages/All/py311-plotly-5.24.1_1.pkg
[142i386-default-job-08] Installing py311-plotly-5.24.1_1...
[142i386-default-job-08] `-- Installing py311-tenacity-9.0.0...
[142i386-default-job-08] `-- Extracting py311-tenacity-9.0.0: .......... done
[142i386-default-job-08] Extracting py311-plotly-5.24.1_1: .......... done
===> py311-pymatgen-2025.6.14_1 depends on package: py311-plotly>=5.0.0 - found
===> Returning to build of py311-pymatgen-2025.6.14_1
===> py311-pymatgen-2025.6.14_1 depends on package: py311-pybtex>=0.24.0 - not found
===> Installing existing package /packages/All/py311-pybtex-0.25.1.pkg
[142i386-default-job-08] Installing py311-pybtex-0.25.1...
[142i386-default-job-08] `-- Installing py311-latexcodec-3.0.1...
[142i386-default-job-08] `-- Extracting py311-latexcodec-3.0.1: .......... done
[142i386-default-job-08] Extracting py311-pybtex-0.25.1: .......... done
===> py311-pymatgen-2025.6.14_1 depends on package: py311-pybtex>=0.24.0 - found
===> Returning to build of py311-pymatgen-2025.6.14_1
===> py311-pymatgen-2025.6.14_1 depends on package: py311-requests>=2.32 - found
===> py311-pymatgen-2025.6.14_1 depends on package: py311-ruamel.yaml>=0.17.0 - found
===> py311-pymatgen-2025.6.14_1 depends on package: py311-scipy>=1.13.0 - found
===> py311-pymatgen-2025.6.14_1 depends on package: py311-spglib>=2.5 - not found
===> Installing existing package /packages/All/py311-spglib-2.6.0.pkg
[142i386-default-job-08] Installing py311-spglib-2.6.0...
[142i386-default-job-08] `-- Installing spglib-2.6.0...
[142i386-default-job-08] `-- Extracting spglib-2.6.0: .......... done
[142i386-default-job-08] Extracting py311-spglib-2.6.0: .......... done
===> py311-pymatgen-2025.6.14_1 depends on package: py311-spglib>=2.5 - found
===> Returning to build of py311-pymatgen-2025.6.14_1
===> py311-pymatgen-2025.6.14_1 depends on package: py311-sympy>=1.3 - not found
===> Installing existing package /packages/All/py311-sympy-1.14.0.pkg
[142i386-default-job-08] Installing py311-sympy-1.14.0...
[142i386-default-job-08] `-- Installing py311-mpmath-1.3.0_2...
[142i386-default-job-08] | `-- Installing py311-gmpy2-2.2.1_1...
[142i386-default-job-08] | `-- Extracting py311-gmpy2-2.2.1_1: .......... done
[142i386-default-job-08] `-- Extracting py311-mpmath-1.3.0_2: .......... done
[142i386-default-job-08] Extracting py311-sympy-1.14.0: .......... done
===> py311-pymatgen-2025.6.14_1 depends on package: py311-sympy>=1.3 - found
===> Returning to build of py311-pymatgen-2025.6.14_1
===> py311-pymatgen-2025.6.14_1 depends on package: py311-tabulate>=0.9 - not found
===> Installing existing package /packages/All/py311-tabulate-0.9.0.pkg
[142i386-default-job-08] Installing py311-tabulate-0.9.0...
[142i386-default-job-08] Extracting py311-tabulate-0.9.0: .......... done
===> py311-pymatgen-2025.6.14_1 depends on package: py311-tabulate>=0.9 - found
===> Returning to build of py311-pymatgen-2025.6.14_1
===> py311-pymatgen-2025.6.14_1 depends on package: py311-tqdm>=4.60 - found
===> py311-pymatgen-2025.6.14_1 depends on package: py311-uncertainties>=3.1.4 - not found
===> Installing existing package /packages/All/py311-uncertainties-3.2.2.pkg
[142i386-default-job-08] Installing py311-uncertainties-3.2.2...
[142i386-default-job-08] `-- Installing py311-future-0.18.3_1...
[142i386-default-job-08] `-- Extracting py311-future-0.18.3_1: .......... done
[142i386-default-job-08] Extracting py311-uncertainties-3.2.2: .......... done
===> py311-pymatgen-2025.6.14_1 depends on package: py311-uncertainties>=3.1.4 - found
===> Returning to build of py311-pymatgen-2025.6.14_1
===> py311-pymatgen-2025.6.14_1 depends on package: py311-ase>=3.23.0 - not found
===> Installing existing package /packages/All/py311-ase-3.26.0.pkg
[142i386-default-job-08] Installing py311-ase-3.26.0...
[142i386-default-job-08] Extracting py311-ase-3.26.0: .......... done
===> py311-pymatgen-2025.6.14_1 depends on package: py311-ase>=3.23.0 - found
===> Returning to build of py311-pymatgen-2025.6.14_1
===> py311-pymatgen-2025.6.14_1 depends on package: py311-beautifulsoup>0 - not found
===> Installing existing package /packages/All/py311-beautifulsoup-4.13.4_1.pkg
[142i386-default-job-08] Installing py311-beautifulsoup-4.13.4_1...
[142i386-default-job-08] `-- Installing py311-html5lib-1.1_1...
[142i386-default-job-08] | `-- Installing py311-webencodings-0.5.1_1...
[142i386-default-job-08] | `-- Extracting py311-webencodings-0.5.1_1: .......... done
[142i386-default-job-08] `-- Extracting py311-html5lib-1.1_1: .......... done
[142i386-default-job-08] `-- 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-beautifulsoup-4.13.4_1.pkg
*** Error code 1
Stop.
make: stopped in /usr/ports/science/py-pymatgen