[package - main-amd64-default][biology/py-PySCeS] Failed for py39-PySCeS-1.1.1 in build
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Date: Sun, 12 Nov 2023 07:55:07 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/pae2c790c6a86_s105c7c4b8d/logs/py39-PySCeS-1.1.1.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=pae2c790c6a86_s105c7c4b8d
Log:
=>> Building biology/py-PySCeS
build started at Sun Nov 12 07:54:58 UTC 2023
port directory: /usr/ports/biology/py-PySCeS
package name: py39-PySCeS-1.1.1
building for: FreeBSD main-amd64-default-job-12 15.0-CURRENT FreeBSD 15.0-CURRENT 1500003 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1385 Jul 29 01:01 /usr/ports/biology/py-PySCeS/Makefile
Ports top last git commit: ae2c790c6a8
Ports top unclean checkout: no
Port dir last git commit: 3cea739c6a8
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.3.0-1251-ge8a0e12e
Host OSVERSION: 1500000
Jail OSVERSION: 1500003
Job Id: 12
!!! Jail is newer than host. (Jail: 1500003, Host: 1500000) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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PORT_FLAGS=
PKGENV=
FLAVOR=py39
MAKE_ARGS= FLAVOR=py39
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
F77="gfortran12" F90="gfortran12" FC="gfortran12" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc12" PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/.cache HOME=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
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--End MAKE_ENV--
--PLIST_SUB--
PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/PySCeS" EXAMPLESDIR="share/examples/PySCeS" DATADIR="share/PySCeS" WWWDIR="www/PySCeS" ETCDIR="etc/PySCeS"
--End PLIST_SUB--
--SUB_LIST--
PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd15 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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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.
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# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
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max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
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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 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-1.20.8.pkg
[main-amd64-default-job-12] Installing pkg-1.20.8...
[main-amd64-default-job-12] Extracting pkg-1.20.8: .......... 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
[main-amd64-default-job-12] Installing py39-scikit-build-0.16.7_1...
[main-amd64-default-job-12] `-- Installing py39-distro-1.8.0_2...
[main-amd64-default-job-12] | `-- Installing python39-3.9.18...
[main-amd64-default-job-12] | | `-- Installing gettext-runtime-0.22.3...
[main-amd64-default-job-12] | | `-- Installing indexinfo-0.3.1...
[main-amd64-default-job-12] | | `-- Extracting indexinfo-0.3.1: .... done
[main-amd64-default-job-12] | | `-- Extracting gettext-runtime-0.22.3: .......... done
[main-amd64-default-job-12] | | `-- Installing libffi-3.4.4...
[main-amd64-default-job-12] | | `-- Extracting libffi-3.4.4: .......... done
[main-amd64-default-job-12] | | `-- Installing mpdecimal-2.5.1...
[main-amd64-default-job-12] | | `-- Extracting mpdecimal-2.5.1: .......... done
[main-amd64-default-job-12] | | `-- Installing readline-8.2.1...
[main-amd64-default-job-12] | | `-- Extracting readline-8.2.1: .......... done
[main-amd64-default-job-12] | `-- Extracting python39-3.9.18: .......... done
[main-amd64-default-job-12] `-- Extracting py39-distro-1.8.0_2: .......... done
[main-amd64-default-job-12] `-- Installing py39-packaging-23.2...
<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
[main-amd64-default-job-12] Installing py39-scipy-1.11.1...
[main-amd64-default-job-12] `-- Installing blas-3.11.0_1...
[main-amd64-default-job-12] `-- Extracting blas-3.11.0_1: ........ done
[main-amd64-default-job-12] 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-jCFIEC'
Run Build Command(s): /usr/local/bin/cmake -E env VERBOSE=1 /usr/bin/make -f Makefile cmTC_8f33d/fast
/usr/bin/make -f CMakeFiles/cmTC_8f33d.dir/build.make CMakeFiles/cmTC_8f33d.dir/build
Building C object CMakeFiles/cmTC_8f33d.dir/testCCompiler.c.o
/usr/bin/cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT CMakeFiles/cmTC_8f33d.dir/testCCompiler.c.o -MF CMakeFiles/cmTC_8f33d.dir/testCCompiler.c.o.d -o CMakeFiles/cmTC_8f33d.dir/testCCompiler.c.o -c /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.1.1/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-jCFIEC/testCCompiler.c
Linking C executable cmTC_8f33d
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_8f33d.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_8f33d.dir/testCCompiler.c.o -o cmTC_8f33d
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-jCFIEC
*** 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-jCFIEC
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