[package - main-amd64-default][science/py-spglib] Failed for py311-spglib-2.5.0_1 in build
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Date: Sat, 01 Mar 2025 05:15:44 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/beefy18/data/main-amd64-default/pe7b7ad617ba1_se2dd73cf45a/logs/py311-spglib-2.5.0_1.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=pe7b7ad617ba1_se2dd73cf45a
Log:
=>> Building science/py-spglib
build started at Sat Mar 1 05:15:36 UTC 2025
port directory: /usr/ports/science/py-spglib
package name: py311-spglib-2.5.0_1
building for: FreeBSD main-amd64-default-job-11 15.0-CURRENT FreeBSD 15.0-CURRENT 1500033 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1072 Sep 14 01:01 /usr/ports/science/py-spglib/Makefile
Ports top last git commit: e7b7ad617ba
Ports top unclean checkout: no
Port dir last git commit: 5001da995c7
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500028
Jail OSVERSION: 1500033
Job Id: 11
!!! Jail is newer than host. (Jail: 1500033, Host: 1500028) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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PKGENV=
FLAVOR=py311
MAKE_ARGS= FLAVOR=py311
---End Poudriere Port Flags/Env---
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---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/science/py-spglib/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-spglib/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-spglib/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-spglib/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-spglib/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-spglib/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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--PLIST_SUB--
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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_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/spglib DOCSDIR=/usr/local/share/doc/spglib EXAMPLESDIR=/usr/local/share/examples/spglib WWWDIR=/usr/local/www/spglib ETCDIR=/usr/local/etc/spglib
--End SUB_LIST--
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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.
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MAKE_JOBS_NUMBER=3
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UID=0
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open files (-n) 8192
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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-spglib-2.5.0_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.0.6.pkg
[main-amd64-default-job-11] Installing pkg-2.0.6...
[main-amd64-default-job-11] Extracting pkg-2.0.6: .......... done
===> py311-spglib-2.5.0_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py311-spglib-2.5.0_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 BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py311-spglib-2.5.0_1 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-spglib-2.5.0_1 for building
=> SHA256 Checksum OK for spglib-spglib-v2.5.0_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-spglib-2.5.0_1 for building
===> Extracting for py311-spglib-2.5.0_1
=> SHA256 Checksum OK for spglib-spglib-v2.5.0_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-spglib-2.5.0_1
===> Applying FreeBSD patches for py311-spglib-2.5.0_1 from /usr/ports/science/py-spglib/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-spglib-2.5.0_1 depends on package: py311-setuptools-scm>0 - not found
===> Installing existing package /packages/All/py311-setuptools-scm-8.0.4.pkg
[main-amd64-default-job-11] Installing py311-setuptools-scm-8.0.4...
[main-amd64-default-job-11] `-- Installing py311-packaging-24.2...
[main-amd64-default-job-11] | `-- Installing python311-3.11.11...
[main-amd64-default-job-11] | | `-- Installing gettext-runtime-0.23.1...
[main-amd64-default-job-11] | | `-- Installing indexinfo-0.3.1_1...
[main-amd64-default-job-11] | | `-- Extracting indexinfo-0.3.1_1: .... done
[main-amd64-default-job-11] | | `-- Extracting gettext-runtime-0.23.1: .......... done
[main-amd64-default-job-11] | | `-- Installing libffi-3.4.6...
[main-amd64-default-job-11] | | `-- Extracting libffi-3.4.6: .......... done
[main-amd64-default-job-11] | | `-- Installing mpdecimal-4.0.0...
[main-amd64-default-job-11] | | `-- Extracting mpdecimal-4.0.0: .......... done
[main-amd64-default-job-11] | | `-- Installing readline-8.2.13_2...
[main-amd64-default-job-11] | | `-- Extracting readline-8.2.13_2: .......... done
[main-amd64-default-job-11] | `-- Extracting python311-3.11.11: .......... done
[main-amd64-default-job-11] `-- Extracting py311-packaging-24.2: .......... done
[main-amd64-default-job-11] `-- Installing py311-typing-extensions-4.12.2...
[main-amd64-default-job-11] `-- Extracting py311-typing-extensions-4.12.2: .......... done
[main-amd64-default-job-11] Extracting py311-setuptools-scm-8.0.4: .......... 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-spglib-2.5.0_1 depends on package: py311-setuptools-scm>0 - found
===> Returning to build of py311-spglib-2.5.0_1
===> py311-spglib-2.5.0_1 depends on package: py311-scikit-build-core>0 - not found
===> Installing existing package /packages/All/py311-scikit-build-core-0.11.0.pkg
[main-amd64-default-job-11] Installing py311-scikit-build-core-0.11.0...
[main-amd64-default-job-11] `-- Installing py311-pathspec-0.12.1...
[main-amd64-default-job-11] `-- Extracting py311-pathspec-0.12.1: .......... done
[main-amd64-default-job-11] Extracting py311-scikit-build-core-0.11.0: .......... done
===> py311-spglib-2.5.0_1 depends on package: py311-scikit-build-core>0 - found
===> Returning to build of py311-spglib-2.5.0_1
===> py311-spglib-2.5.0_1 depends on package: py311-pyproject-metadata>0 - not found
===> Installing existing package /packages/All/py311-pyproject-metadata-0.7.1.pkg
[main-amd64-default-job-11] Installing py311-pyproject-metadata-0.7.1...
[main-amd64-default-job-11] Extracting py311-pyproject-metadata-0.7.1: .......... done
===> py311-spglib-2.5.0_1 depends on package: py311-pyproject-metadata>0 - found
===> Returning to build of py311-spglib-2.5.0_1
===> py311-spglib-2.5.0_1 depends on executable: cmake - not found
===> Installing existing package /packages/All/cmake-core-3.31.6.pkg
[main-amd64-default-job-11] Installing cmake-core-3.31.6...
[main-amd64-default-job-11] `-- Installing expat-2.6.4...
[main-amd64-default-job-11] `-- Extracting expat-2.6.4: .......... done
[main-amd64-default-job-11] `-- Installing jsoncpp-1.9.6_1...
[main-amd64-default-job-11] `-- Extracting jsoncpp-1.9.6_1: .......... done
[main-amd64-default-job-11] `-- Installing libidn2-2.3.7...
[main-amd64-default-job-11] | `-- Installing libunistring-1.3...
[main-amd64-default-job-11] | `-- Extracting libunistring-1.3: .......... done
[main-amd64-default-job-11] `-- Extracting libidn2-2.3.7: .......... done
[main-amd64-default-job-11] `-- Installing libuv-1.50.0...
[main-amd64-default-job-11] `-- Extracting libuv-1.50.0: .......... done
[main-amd64-default-job-11] `-- Installing rhash-1.4.4_1...
[main-amd64-default-job-11] `-- Extracting rhash-1.4.4_1: .......... done
[main-amd64-default-job-11] Extracting cmake-core-3.31.6: .......... done
===> py311-spglib-2.5.0_1 depends on executable: cmake - found
===> Returning to build of py311-spglib-2.5.0_1
===> py311-spglib-2.5.0_1 depends on package: py311-numpy>=1.16,1<1.27,1 - not found
===> Installing existing package /packages/All/py311-numpy-1.26.4_5,1.pkg
[main-amd64-default-job-11] Installing py311-numpy-1.26.4_5,1...
[main-amd64-default-job-11] `-- Installing gcc13-13.3.0...
[main-amd64-default-job-11] | `-- Installing binutils-2.44,1...
[main-amd64-default-job-11] | | `-- Installing zstd-1.5.7...
[main-amd64-default-job-11] | | `-- Installing liblz4-1.10.0,1...
[main-amd64-default-job-11] | | `-- Extracting liblz4-1.10.0,1: .......... done
[main-amd64-default-job-11] | | `-- Extracting zstd-1.5.7: .......... done
[main-amd64-default-job-11] | `-- Extracting binutils-2.44,1: .......... done
[main-amd64-default-job-11] | `-- Installing gmp-6.3.0...
[main-amd64-default-job-11] | `-- Extracting gmp-6.3.0: .......... done
[main-amd64-default-job-11] | `-- Installing mpc-1.3.1_1...
[main-amd64-default-job-11] | | `-- Installing mpfr-4.2.1,1...
[main-amd64-default-job-11] | | `-- Extracting mpfr-4.2.1,1: .......... done
[main-amd64-default-job-11] | `-- Extracting mpc-1.3.1_1: ......... done
[main-amd64-default-job-11] `-- Extracting gcc13-13.3.0: .......... done
[main-amd64-default-job-11] `-- Installing openblas-0.3.29_1,2...
[main-amd64-default-job-11] `-- Extracting openblas-0.3.29_1,2: .......... done
[main-amd64-default-job-11] `-- Installing py311-setuptools-63.1.0_1...
[main-amd64-default-job-11] `-- Extracting py311-setuptools-63.1.0_1: .......... done
[main-amd64-default-job-11] `-- Installing suitesparse-umfpack-6.3.5_1...
[main-amd64-default-job-11] | `-- Installing suitesparse-amd-3.3.3...
[main-amd64-default-job-11] | | `-- Installing suitesparse-config-7.8.3_1...
[main-amd64-default-job-11] | | `-- Extracting suitesparse-config-7.8.3_1: .......... done
[main-amd64-default-job-11] | `-- Extracting suitesparse-amd-3.3.3: .......... done
[main-amd64-default-job-11] | `-- Installing suitesparse-camd-3.3.3...
[main-amd64-default-job-11] | `-- Extracting suitesparse-camd-3.3.3: .......... done
[main-amd64-default-job-11] | `-- Installing suitesparse-ccolamd-3.3.4...
[main-amd64-default-job-11] | `-- Extracting suitesparse-ccolamd-3.3.4: .......... done
[main-amd64-default-job-11] | `-- Installing suitesparse-cholmod-5.3.0_1...
[main-amd64-default-job-11] | | `-- Installing suitesparse-colamd-3.3.4...
[main-amd64-default-job-11] | | `-- Extracting suitesparse-colamd-3.3.4: .......... done
[main-amd64-default-job-11] | `-- Extracting suitesparse-cholmod-5.3.0_1: .......... done
[main-amd64-default-job-11] `-- Extracting suitesparse-umfpack-6.3.5_1: .......... done
[main-amd64-default-job-11] Extracting py311-numpy-1.26.4_5,1: .......... done
=====
Message from gcc13-13.3.0:
--
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-spglib-2.5.0_1 depends on package: py311-numpy>=1.16,1<1.27,1 - found
===> Returning to build of py311-spglib-2.5.0_1
===> py311-spglib-2.5.0_1 depends on package: py311-setuptools>0 - found
===> py311-spglib-2.5.0_1 depends on file: /usr/local/bin/python3.11 - found
===> py311-spglib-2.5.0_1 depends on package: py311-build>=0 - not found
===> Installing existing package /packages/All/py311-build-1.2.2_2.pkg
[main-amd64-default-job-11] Installing py311-build-1.2.2_2...
[main-amd64-default-job-11] `-- Installing py311-pyproject-hooks-1.2.0...
[main-amd64-default-job-11] `-- Extracting py311-pyproject-hooks-1.2.0: .......... done
[main-amd64-default-job-11] Extracting py311-build-1.2.2_2: .......... done
===> py311-spglib-2.5.0_1 depends on package: py311-build>=0 - found
===> Returning to build of py311-spglib-2.5.0_1
===> py311-spglib-2.5.0_1 depends on package: py311-installer>=0 - not found
===> Installing existing package /packages/All/py311-installer-0.7.0.pkg
[main-amd64-default-job-11] Installing py311-installer-0.7.0...
[main-amd64-default-job-11] Extracting py311-installer-0.7.0: .......... done
===> py311-spglib-2.5.0_1 depends on package: py311-installer>=0 - found
===> Returning to build of py311-spglib-2.5.0_1
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-spglib-2.5.0_1 depends on shared library: libsymspg.so - not found
===> Installing existing package /packages/All/spglib-2.5.0.pkg
[main-amd64-default-job-11] Installing spglib-2.5.0...
[main-amd64-default-job-11] Extracting spglib-2.5.0: .......... done
===> py311-spglib-2.5.0_1 depends on shared library: libsymspg.so - found (/usr/local/lib/libsymspg.so)
===> Returning to build of py311-spglib-2.5.0_1
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for py311-spglib-2.5.0_1
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for py311-spglib-2.5.0_1
* Getting build dependencies for wheel...
* Building wheel...
+ Exception Group Traceback (most recent call last):
| File "/usr/local/lib/python3.11/site-packages/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
| main()
| File "/usr/local/lib/python3.11/site-packages/pyproject_hooks/_in_process/_in_process.py", line 373, in main
| json_out["return_val"] = hook(**hook_input["kwargs"])
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/site-packages/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel
| return _build_backend().build_wheel(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/site-packages/scikit_build_core/build/__init__.py", line 33, in build_wheel
| return _build_wheel_impl(
| ^^^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/site-packages/scikit_build_core/build/wheel.py", line 174, in _build_wheel_impl
| return _build_wheel_impl_impl(
| ^^^^^^^^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/site-packages/scikit_build_core/build/wheel.py", line 231, in _build_wheel_impl_impl
| metadata = get_standard_metadata(pyproject, settings)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/site-packages/scikit_build_core/build/metadata.py", line 75, in get_standard_metadata
| metadata = StandardMetadata.from_pyproject(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/site-packages/scikit_build_core/_vendor/pyproject_metadata/__init__.py", line 432, in from_pyproject
| pyproject.finalize("Failed to parse pyproject.toml")
| File "/usr/local/lib/python3.11/site-packages/scikit_build_core/_vendor/pyproject_metadata/errors.py", line 108, in finalize
| raise ExceptionGroup(msg, self.errors)
| ExceptionGroup: Failed to parse pyproject.toml (1 sub-exception)
+-+---------------- 1 ----------------
| scikit_build_core._vendor.pyproject_metadata.errors.ConfigurationError: Field "project.license-files" has an invalid type, expecting a list of strings (got dict)
+------------------------------------
ERROR Backend subprocess exited when trying to invoke build_wheel
*** Error code 1
Stop.
make: stopped making "build" in /usr/ports/science/py-spglib