[package - 140amd64-default][biology/py-PySCeS] Failed for py39-PySCeS-1.1.1 in build
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Date: Fri, 15 Dec 2023 01:56:28 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/beefy12/data/140amd64-default/bb504ccec5fc/logs/py39-PySCeS-1.1.1.log
Build URL: https://pkg-status.freebsd.org/beefy12/build.html?mastername=140amd64-default&build=bb504ccec5fc
Log:
=>> Building biology/py-PySCeS
build started at Fri Dec 15 01:56:13 UTC 2023
port directory: /usr/ports/biology/py-PySCeS
package name: py39-PySCeS-1.1.1
building for: FreeBSD 140amd64-default-job-03 14.0-RELEASE-p2 FreeBSD 14.0-RELEASE-p2 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1385 Aug 26 01:01 /usr/ports/biology/py-PySCeS/Makefile
Ports top last git commit: bb504ccec5
Ports top unclean checkout: no
Port dir last git commit: 157c391cc1
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.3.0-1258-gbc38e2e6
Host OSVERSION: 1500006
Jail OSVERSION: 1400097
Job Id: 03
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--PLIST_SUB--
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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/PySCeS DOCSDIR=/usr/local/share/doc/PySCeS EXAMPLESDIR=/usr/local/share/examples/PySCeS WWWDIR=/usr/local/www/PySCeS ETCDIR=/usr/local/etc/PySCeS
--End SUB_LIST--
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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 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
===> py39-PySCeS-1.1.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.9.pkg
[140amd64-default-job-03] Installing pkg-1.20.9...
[140amd64-default-job-03] Extracting pkg-1.20.9: .......... done
===> py39-PySCeS-1.1.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py39-PySCeS-1.1.1
===========================================================================
=======================<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 py39-PySCeS-1.1.1 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 py39-PySCeS-1.1.1 for building
=> SHA256 Checksum OK for pysces-1.1.1.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 py39-PySCeS-1.1.1 for building
===> Extracting for py39-PySCeS-1.1.1
=> SHA256 Checksum OK for pysces-1.1.1.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-PySCeS-1.1.1
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py39-PySCeS-1.1.1 depends on package: py39-scikit-build>0 - not found
===> Installing existing package /packages/All/py39-scikit-build-0.16.7_1.pkg
[140amd64-default-job-03] Installing py39-scikit-build-0.16.7_1...
[140amd64-default-job-03] `-- Installing py39-distro-1.8.0_2...
[140amd64-default-job-03] | `-- Installing python39-3.9.18...
[140amd64-default-job-03] | | `-- Installing gettext-runtime-0.22.3...
[140amd64-default-job-03] | | `-- Installing indexinfo-0.3.1...
[140amd64-default-job-03] | | `-- Extracting indexinfo-0.3.1: .... done
[140amd64-default-job-03] | | `-- Extracting gettext-runtime-0.22.3: .......... done
[140amd64-default-job-03] | | `-- Installing libffi-3.4.4...
[140amd64-default-job-03] | | `-- Extracting libffi-3.4.4: .......... done
[140amd64-default-job-03] | | `-- Installing mpdecimal-2.5.1...
[140amd64-default-job-03] | | `-- Extracting mpdecimal-2.5.1: .......... done
[140amd64-default-job-03] | | `-- Installing readline-8.2.1...
[140amd64-default-job-03] | | `-- Extracting readline-8.2.1: .......... done
[140amd64-default-job-03] | `-- Extracting python39-3.9.18: .......... done
[140amd64-default-job-03] `-- Extracting py39-distro-1.8.0_2: .......... done
[140amd64-default-job-03] `-- Installing py39-packaging-23.2...
[140amd64-default-job-03] `-- Extracting py39-packaging-23.2: .......... done
[140amd64-default-job-03] `-- Installing py39-wheel-0.42.0...
[140amd64-default-job-03] `-- Extracting py39-wheel-0.42.0: .......... done
[140amd64-default-job-03] Extracting py39-scikit-build-0.16.7_1: .......... done
=====
Message from python39-3.9.18:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
<snip>
driver properties. Example:
FREETYPE_PROPERTIES=truetype:interpreter-version=35 \
cff:no-stem-darkening=1 \
autofitter:warping=1
This allows to select, say, the subpixel hinting mode at runtime for a given
application.
If LONG_PCF_NAMES port's option was enabled, the PCF family names may include
the foundry and information whether they contain wide characters. For example,
"Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at
run time with using pcf:no-long-family-names property, if needed. Example:
FREETYPE_PROPERTIES=pcf:no-long-family-names=1
How to recreate fontconfig cache with using such environment variable,
if needed:
# env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv
The controllable properties are listed in the section "Controlling FreeType
Modules" in the reference's table of contents
(/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed).
===> py39-PySCeS-1.1.1 depends on package: py39-matplotlib>0 - found
===> Returning to build of py39-PySCeS-1.1.1
===> py39-PySCeS-1.1.1 depends on package: py39-scipy>0 - not found
===> Installing existing package /packages/All/py39-scipy-1.11.1.pkg
[140amd64-default-job-03] Installing py39-scipy-1.11.1...
[140amd64-default-job-03] `-- Installing blas-3.11.0_1...
[140amd64-default-job-03] `-- Extracting blas-3.11.0_1: ........ done
[140amd64-default-job-03] Extracting py39-scipy-1.11.1: .......... done
===> py39-PySCeS-1.1.1 depends on package: py39-scipy>0 - found
===> Returning to build of py39-PySCeS-1.1.1
===> py39-PySCeS-1.1.1 depends on executable: gfortran12 - found
===> py39-PySCeS-1.1.1 depends on package: py39-setuptools>=63.1.0 - found
===> py39-PySCeS-1.1.1 depends on file: /usr/local/bin/python3.9 - found
===> py39-PySCeS-1.1.1 depends on file: /usr/local/bin/as - 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 py39-PySCeS-1.1.1
setuptools is available.
bdist_conda not available.
'install_dir' :: /usr/local/lib/python3.9/site-packages/pysces
'model_dir' :: /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/Pysces/psc
'output_dir' :: /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/Pysces
'gnuplot_dir' :: None
'silentstart' :: False
'change_dir_on_start' :: False
'custom_datatype' :: None
Default configuration file installed
Building pitcon
Building nleq2
running config
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for py39-PySCeS-1.1.1
setuptools is available.
bdist_conda not available.
'install_dir' :: /usr/local/lib/python3.9/site-packages/pysces
'model_dir' :: /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/Pysces/psc
'output_dir' :: /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/Pysces
'gnuplot_dir' :: None
'silentstart' :: False
'change_dir_on_start' :: False
'custom_datatype' :: None
Default configuration file installed
Building pitcon
Building nleq2
--------------------------------------------------------------------------------
-- Trying 'Ninja' generator
--------------------------------
---------------------------
----------------------
-----------------
------------
-------
--
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
Not searching for unused variables given on the command line.
CMake Error: CMake was unable to find a build program corresponding to "Ninja". CMAKE_MAKE_PROGRAM is not set. You probably need to select a different build tool.
-- Configuring incomplete, errors occurred!
--
-------
------------
-----------------
----------------------
---------------------------
--------------------------------
-- Trying 'Ninja' generator - failure
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-- Trying 'Unix Makefiles' generator
--------------------------------
---------------------------
----------------------
-----------------
------------
-------
--
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
Not searching for unused variables given on the command line.
-- The C compiler identification is Clang 16.0.6
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - failed
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc - broken
CMake Error at /usr/local/share/cmake/Modules/CMakeTestCCompiler.cmake:67 (message):
The C compiler
"/usr/bin/cc"
is not able to compile a simple test program.
It fails with the following output:
Change Dir: '/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.1.1/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-NDIxi6'
Run Build Command(s): /usr/local/bin/cmake -E env VERBOSE=1 /usr/bin/make -f Makefile cmTC_5abc6/fast
/usr/bin/make -f CMakeFiles/cmTC_5abc6.dir/build.make CMakeFiles/cmTC_5abc6.dir/build
Building C object CMakeFiles/cmTC_5abc6.dir/testCCompiler.c.o
/usr/bin/cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT CMakeFiles/cmTC_5abc6.dir/testCCompiler.c.o -MF CMakeFiles/cmTC_5abc6.dir/testCCompiler.c.o.d -o CMakeFiles/cmTC_5abc6.dir/testCCompiler.c.o -c /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.1.1/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-NDIxi6/testCCompiler.c
Linking C executable cmTC_5abc6
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_5abc6.dir/link.txt --verbose=1
/usr/bin/cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpython3.9 -shared -Wl,-rpath=/usr/local/lib/gcc12 -L/usr/local/lib/gcc12 -fstack-protector-strong CMakeFiles/cmTC_5abc6.dir/testCCompiler.c.o -o cmTC_5abc6
ld: error: unable to find library -lpython3.9
cc: error: linker command failed with exit code 1 (use -v to see invocation)
*** Error code 1
Stop.
make[2]: stopped in /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.1.1/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-NDIxi6
*** Error code 1
Stop.
make[1]: stopped in /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.1.1/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-NDIxi6
CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
CMakeLists.txt:3 (ENABLE_LANGUAGE)
-- Configuring incomplete, errors occurred!
--
-------
------------
-----------------
----------------------
---------------------------
--------------------------------
-- Trying 'Unix Makefiles' generator - failure
--------------------------------------------------------------------------------
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "setup.py", line 185, in <module>
setup(
File "/usr/local/lib/python3.9/site-packages/skbuild/setuptools_wrap.py", line 634, in setup
env = cmkr.configure(
File "/usr/local/lib/python3.9/site-packages/skbuild/cmaker.py", line 236, in configure
generator = self.platform.get_best_generator(
File "/usr/local/lib/python3.9/site-packages/skbuild/platform_specifics/abstract.py", line 182, in get_best_generator
.format(line="*" * 80, installation_help=self.generator_installation_help)
File "/usr/local/lib/python3.9/site-packages/skbuild/platform_specifics/abstract.py", line 42, in generator_installation_help
raise NotImplementedError # pragma: no cover
NotImplementedError
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/py-PySCeS