[package - 140amd64-default][devel/py-pykdtree] Failed for py39-pykdtree-1.3.10 in build
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Date: Fri, 16 Feb 2024 10:42:45 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: sunpoet@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy12/data/140amd64-default/e9c9c73181b5/logs/py39-pykdtree-1.3.10.log
Build URL: https://pkg-status.freebsd.org/beefy12/build.html?mastername=140amd64-default&build=e9c9c73181b5
Log:
=>> Building devel/py-pykdtree
build started at Fri Feb 16 10:42:18 UTC 2024
port directory: /usr/ports/devel/py-pykdtree
package name: py39-pykdtree-1.3.10
building for: FreeBSD 140amd64-default-job-06 14.0-RELEASE-p4 FreeBSD 14.0-RELEASE-p4 amd64
maintained by: sunpoet@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 791 Dec 2 01:02 /usr/ports/devel/py-pykdtree/Makefile
Ports top last git commit: e9c9c73181
Ports top unclean checkout: no
Port dir last git commit: 3175703fdb
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1
Host OSVERSION: 1500006
Jail OSVERSION: 1400097
Job Id: 06
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MAKE_ARGS= FLAVOR=py39
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
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--MAINTAINER--
sunpoet@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/devel/py-pykdtree/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/devel/py-pykdtree/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/devel/py-pykdtree/work-py39/.cache HOME=/wrkdirs/usr/ports/devel/py-pykdtree/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/devel/py-pykdtree/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/devel/py-pykdtree/work-py39/.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/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py39-pykdtree DOCSDIR=/usr/local/share/doc/py39-pykdtree EXAMPLESDIR=/usr/local/share/examples/py39-pykdtree WWWDIR=/usr/local/www/py39-pykdtree ETCDIR=/usr/local/etc/py39-pykdtree
--End SUB_LIST--
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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 ####
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GID=0
UID=0
---End make.conf---
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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 LGPL3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py39-pykdtree-1.3.10 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.9_1.pkg
[140amd64-default-job-06] Installing pkg-1.20.9_1...
[140amd64-default-job-06] Extracting pkg-1.20.9_1: .......... done
===> py39-pykdtree-1.3.10 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py39-pykdtree-1.3.10
===========================================================================
=======================<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 LGPL3 accepted by the user
===> Fetching all distfiles required by py39-pykdtree-1.3.10 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by py39-pykdtree-1.3.10 for building
=> SHA256 Checksum OK for pykdtree-1.3.10.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 LGPL3 accepted by the user
===> Fetching all distfiles required by py39-pykdtree-1.3.10 for building
===> Extracting for py39-pykdtree-1.3.10
=> SHA256 Checksum OK for pykdtree-1.3.10.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 py39-pykdtree-1.3.10
===> Applying FreeBSD patches for py39-pykdtree-1.3.10 from /usr/ports/devel/py-pykdtree/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py39-pykdtree-1.3.10 depends on package: py39-numpy>=0,1 - not found
===> Installing existing package /packages/All/py39-numpy-1.25.0_6,1.pkg
[140amd64-default-job-06] Installing py39-numpy-1.25.0_6,1...
[140amd64-default-job-06] `-- Installing gcc12-12.3.0...
[140amd64-default-job-06] | `-- Installing binutils-2.40_5,1...
[140amd64-default-job-06] | | `-- Installing gettext-runtime-0.22.3_1...
[140amd64-default-job-06] | | `-- Installing indexinfo-0.3.1...
[140amd64-default-job-06] | | `-- Extracting indexinfo-0.3.1: .... done
[140amd64-default-job-06] | | `-- Extracting gettext-runtime-0.22.3_1: .......... done
[140amd64-default-job-06] | | `-- Installing zstd-1.5.5_1...
[140amd64-default-job-06] | | `-- Installing liblz4-1.9.4_1,1...
[140amd64-default-job-06] | | `-- Extracting liblz4-1.9.4_1,1: .......... done
[140amd64-default-job-06] | | `-- Extracting zstd-1.5.5_1: .......... done
[140amd64-default-job-06] | `-- Extracting binutils-2.40_5,1: .......... done
[140amd64-default-job-06] | `-- Installing gmp-6.3.0...
[140amd64-default-job-06] | `-- Extracting gmp-6.3.0: .......... done
[140amd64-default-job-06] | `-- Installing mpc-1.3.1_1...
[140amd64-default-job-06] | | `-- Installing mpfr-4.2.1,1...
[140amd64-default-job-06] | | `-- Extracting mpfr-4.2.1,1: .......... done
[140amd64-default-job-06] | `-- Extracting mpc-1.3.1_1: ......... done
[140amd64-default-job-06] `-- Extracting gcc12-12.3.0: .......... done
[140amd64-default-job-06] `-- Installing openblas-0.3.25,2...
[140amd64-default-job-06] `-- Extracting openblas-0.3.25,2: .......... done
[140amd64-default-job-06] `-- Installing py39-setuptools-63.1.0_1...
[140amd64-default-job-06] | `-- Installing python39-3.9.18_1...
[140amd64-default-job-06] | | `-- Installing libffi-3.4.4_1...
[140amd64-default-job-06] | | `-- Extracting libffi-3.4.4_1: .......... done
[140amd64-default-job-06] | | `-- Installing mpdecimal-2.5.1...
[140amd64-default-job-06] | | `-- Extracting mpdecimal-2.5.1: .......... done
[140amd64-default-job-06] | | `-- Installing readline-8.2.7_1...
[140amd64-default-job-06] | | `-- Extracting readline-8.2.7_1: .......... done
[140amd64-default-job-06] | `-- Extracting python39-3.9.18_1: .......... done
[140amd64-default-job-06] `-- Extracting py39-setuptools-63.1.0_1: .......... done
[140amd64-default-job-06] `-- Installing suitesparse-umfpack-6.3.2...
[140amd64-default-job-06] | `-- Installing suitesparse-amd-3.3.1...
[140amd64-default-job-06] | | `-- Installing suitesparse-config-7.6.0...
[140amd64-default-job-06] | | `-- Extracting suitesparse-config-7.6.0: .......... done
[140amd64-default-job-06] | `-- Extracting suitesparse-amd-3.3.1: .......... done
[140amd64-default-job-06] | `-- Installing suitesparse-camd-3.3.1...
[140amd64-default-job-06] | `-- Extracting suitesparse-camd-3.3.1: .......... done
[140amd64-default-job-06] | `-- Installing suitesparse-ccolamd-3.3.2...
[140amd64-default-job-06] | `-- Extracting suitesparse-ccolamd-3.3.2: .......... done
[140amd64-default-job-06] | `-- Installing suitesparse-cholmod-5.2.0...
[140amd64-default-job-06] | | `-- Installing suitesparse-colamd-3.3.2...
[140amd64-default-job-06] | | `-- Extracting suitesparse-colamd-3.3.2: .......... done
[140amd64-default-job-06] | `-- Extracting suitesparse-cholmod-5.2.0: .......... done
[140amd64-default-job-06] `-- Extracting suitesparse-umfpack-6.3.2: .......... done
[140amd64-default-job-06] Extracting py39-numpy-1.25.0_6,1: .......... done
=====
Message from gcc12-12.3.0:
--
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/gcc12
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
=====
Message from python39-3.9.18_1:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py39-gdbm databases/py-gdbm@py39
py39-sqlite3 databases/py-sqlite3@py39
py39-tkinter x11-toolkits/py-tkinter@py39
===> py39-pykdtree-1.3.10 depends on package: py39-numpy>=0,1 - found
===> Returning to build of py39-pykdtree-1.3.10
===> py39-pykdtree-1.3.10 depends on package: py39-setuptools>=0 - found
===> py39-pykdtree-1.3.10 depends on package: py39-wheel>=0 - not found
===> Installing existing package /packages/All/py39-wheel-0.42.0.pkg
[140amd64-default-job-06] Installing py39-wheel-0.42.0...
[140amd64-default-job-06] Extracting py39-wheel-0.42.0: .......... done
===> py39-pykdtree-1.3.10 depends on package: py39-wheel>=0 - found
===> Returning to build of py39-pykdtree-1.3.10
===> py39-pykdtree-1.3.10 depends on executable: cython-3.9 - not found
===> Installing existing package /packages/All/py39-cython-0.29.37.pkg
[140amd64-default-job-06] Installing py39-cython-0.29.37...
[140amd64-default-job-06] Extracting py39-cython-0.29.37: .......... done
===> py39-pykdtree-1.3.10 depends on executable: cython-3.9 - found
===> Returning to build of py39-pykdtree-1.3.10
===> py39-pykdtree-1.3.10 depends on file: /usr/local/bin/python3.9 - found
===> py39-pykdtree-1.3.10 depends on package: py39-build>=0 - not found
===> Installing existing package /packages/All/py39-build-0.10.0_2.pkg
[140amd64-default-job-06] Installing py39-build-0.10.0_2...
[140amd64-default-job-06] `-- Installing py39-packaging-23.2...
[140amd64-default-job-06] `-- Extracting py39-packaging-23.2: .......... done
[140amd64-default-job-06] `-- Installing py39-pyproject_hooks-1.0.0_2...
[140amd64-default-job-06] | `-- Installing py39-tomli-2.0.1_2...
[140amd64-default-job-06] | `-- Extracting py39-tomli-2.0.1_2: .......... done
[140amd64-default-job-06] `-- Extracting py39-pyproject_hooks-1.0.0_2: .......... done
[140amd64-default-job-06] Extracting py39-build-0.10.0_2: .......... done
===> py39-pykdtree-1.3.10 depends on package: py39-build>=0 - found
===> Returning to build of py39-pykdtree-1.3.10
===> py39-pykdtree-1.3.10 depends on package: py39-installer>=0 - not found
===> Installing existing package /packages/All/py39-installer-0.7.0.pkg
[140amd64-default-job-06] Installing py39-installer-0.7.0...
[140amd64-default-job-06] Extracting py39-installer-0.7.0: .......... done
===> py39-pykdtree-1.3.10 depends on package: py39-installer>=0 - found
===> Returning to build of py39-pykdtree-1.3.10
===========================================================================
=======================<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 py39-pykdtree-1.3.10
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for py39-pykdtree-1.3.10
* Getting build dependencies for wheel...
/usr/local/lib/python3.9/site-packages/setuptools/_distutils/extension.py:134: UserWarning: Unknown Extension options: 'compiler_directions'
warnings.warn(msg)
/usr/local/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /wrkdirs/usr/ports/devel/py-pykdtree/work-py39/pykdtree-1.3.10/pykdtree/kdtree.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Compiling pykdtree/kdtree.pyx because it depends on /usr/local/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd.
[1/1] Cythonizing pykdtree/kdtree.pyx
running egg_info
writing pykdtree.egg-info/PKG-INFO
writing dependency_links to pykdtree.egg-info/dependency_links.txt
writing requirements to pykdtree.egg-info/requires.txt
writing top-level names to pykdtree.egg-info/top_level.txt
reading manifest file 'pykdtree.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'pykdtree/render_template.py'
adding license file 'LICENSE.txt'
writing manifest file 'pykdtree.egg-info/SOURCES.txt'
* Building wheel...
/usr/local/lib/python3.9/site-packages/setuptools/_distutils/extension.py:134: UserWarning: Unknown Extension options: 'compiler_directions'
warnings.warn(msg)
running bdist_wheel
running build
running build_py
creating build
creating build/lib.freebsd-14.0-RELEASE-p4-amd64-cpython-39
creating build/lib.freebsd-14.0-RELEASE-p4-amd64-cpython-39/pykdtree
copying pykdtree/__init__.py -> build/lib.freebsd-14.0-RELEASE-p4-amd64-cpython-39/pykdtree
copying pykdtree/test_tree.py -> build/lib.freebsd-14.0-RELEASE-p4-amd64-cpython-39/pykdtree
running build_ext
Will use gomp for OpenMP.
Compiler: unix / OpenMP: gomp / OpenMP compile args: ['-fopenmp'] / OpenMP link args: ['-lgomp']
building 'pykdtree.kdtree' extension
creating build/temp.freebsd-14.0-RELEASE-p4-amd64-cpython-39
creating build/temp.freebsd-14.0-RELEASE-p4-amd64-cpython-39/pykdtree
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c pykdtree/_kdtree_core.c -o build/temp.freebsd-14.0-RELEASE-p4-amd64-cpython-39/pykdtree/_kdtree_core.o -std=c99 -O3 -fopenmp
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c pykdtree/kdtree.c -o build/temp.freebsd-14.0-RELEASE-p4-amd64-cpython-39/pykdtree/kdtree.o -std=c99 -O3 -fopenmp
pykdtree/kdtree.c:2439:78: error: no member named 'data' in 'struct tagPyArrayObject'
__pyx_v_self->_data_pts_data_float = ((float *)__pyx_v_data_array_float->data);
~~~~~~~~~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:2543:81: error: no member named 'data' in 'struct tagPyArrayObject'
__pyx_v_self->_data_pts_data_double = ((double *)__pyx_v_data_array_double->data);
~~~~~~~~~~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:2582:51: error: no member named 'dimensions' in 'struct tagPyArrayObject'
__pyx_v_self->n = ((uint32_t)(__pyx_v_data_pts->dimensions[0]));
~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:2600:35: error: no member named 'nd' in 'struct tagPyArrayObject'
__pyx_t_1 = ((__pyx_v_data_pts->nd == 1) != 0);
~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:2629:36: error: no member named 'dimensions' in 'struct tagPyArrayObject'
__pyx_t_1 = (((__pyx_v_data_pts->dimensions[1]) > 0x7F) != 0);
~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:2662:54: error: no member named 'dimensions' in 'struct tagPyArrayObject'
__pyx_v_self->ndim = ((int8_t)(__pyx_v_data_pts->dimensions[1]));
~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:3192:36: error: no member named 'nd' in 'struct tagPyArrayObject'
__pyx_t_3 = ((__pyx_v_query_pts->nd == 1) != 0);
~~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:3222:42: error: no member named 'dimensions' in 'struct tagPyArrayObject'
__pyx_v_q_ndim = (__pyx_v_query_pts->dimensions[1]);
~~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:3327:45: error: no member named 'dimensions' in 'struct tagPyArrayObject'
__pyx_v_num_qpoints = (__pyx_v_query_pts->dimensions[0]);
~~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:3396:66: error: no member named 'data' in 'struct tagPyArrayObject'
__pyx_v_closest_idxs_data = ((uint32_t *)__pyx_v_closest_idxs->data);
~~~~~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:3536:63: error: no member named 'data' in 'struct tagPyArrayObject'
__pyx_v_query_mask_data = ((uint8_t *)__pyx_v_query_mask->data);
~~~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:3676:79: error: no member named 'data' in 'struct tagPyArrayObject'
__pyx_v_closest_dists_data_float = ((float *)__pyx_v_closest_dists_float->data);
~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:3756:75: error: no member named 'data' in 'struct tagPyArrayObject'
__pyx_v_query_array_data_float = ((float *)__pyx_v_query_array_float->data);
~~~~~~~~~~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:3845:82: error: no member named 'data' in 'struct tagPyArrayObject'
__pyx_v_closest_dists_data_double = ((double *)__pyx_v_closest_dists_double->data);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
pykdtree/kdtree.c:3925:78: error: no member named 'data' in 'struct tagPyArrayObject'
__pyx_v_query_array_data_double = ((double *)__pyx_v_query_array_double->data);
~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
15 errors generated.
error: command '/usr/bin/cc' failed with exit code 1
ERROR Backend subprocess exited when trying to invoke build_wheel
*** Error code 1
Stop.
make: stopped in /usr/ports/devel/py-pykdtree