[package - main-i386-default][biology/py-PySCeS] Failed for py39-PySCeS-1.0.3 in build
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Date: Tue, 07 Feb 2023 15:57:24 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/beefy17/data/main-i386-default/p96a5483c708f_s77934b7a13/logs/py39-PySCeS-1.0.3.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p96a5483c708f_s77934b7a13
Log:
=>> Building biology/py-PySCeS
build started at Tue Feb 7 15:57:09 UTC 2023
port directory: /usr/ports/biology/py-PySCeS
package name: py39-PySCeS-1.0.3
building for: FreeBSD main-i386-default-job-11 14.0-CURRENT FreeBSD 14.0-CURRENT 1400078 i386
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1400078
Job Id: 11
!!! Jail is newer than host. (Jail: 1400078, Host: 1400073) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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--End PLIST_SUB--
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=======================<phase: check-sanity >============================
===> License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py39-PySCeS-1.0.3 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1.pkg
[main-i386-default-job-11] Installing pkg-1.19.1...
[main-i386-default-job-11] Extracting pkg-1.19.1: .......... done
===> py39-PySCeS-1.0.3 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py39-PySCeS-1.0.3
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py39-PySCeS-1.0.3 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py39-PySCeS-1.0.3 for building
=> SHA256 Checksum OK for pysces-1.0.3.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py39-PySCeS-1.0.3 for building
===> Extracting for py39-PySCeS-1.0.3
=> SHA256 Checksum OK for pysces-1.0.3.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for py39-PySCeS-1.0.3
===========================================================================
=======================<phase: build-depends >============================
===> py39-PySCeS-1.0.3 depends on package: py39-scikit-build>0 - not found
<snip>
----------------------
---------------------------
--------------------------------
-- Trying 'Unix Makefiles' generator - success
--------------------------------------------------------------------------------
Configuring Project
Working directory:
/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.0.3/_skbuild/freebsd-14.0-CURRENT-i386-3.9/cmake-build
Command:
/usr/local/bin/cmake /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.0.3 -G 'Unix Makefiles' -DCMAKE_INSTALL_PREFIX:PATH=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.0.3/_skbuild/freebsd-14.0-CURRENT-i386-3.9/cmake-install -DPYTHON_VERSION_STRING:STRING=3.9.16 -DSKBUILD:INTERNAL=TRUE -DCMAKE_MODULE_PATH:PATH=/usr/local/lib/python3.9/site-packages/skbuild/resources/cmake -DPYTHON_EXECUTABLE:PATH=/usr/local/bin/python3.9 -DPYTHON_INCLUDE_DIR:PATH=/usr/local/include/python3.9 -DPYTHON_LIBRARY:PATH=/usr/local/lib/libpython3.9.so -DPython_EXECUTABLE:PATH=/usr/local/bin/python3.9 -DPython_ROOT_DIR:PATH=/usr/local -DPython_INCLUDE_DIR:PATH=/usr/local/include/python3.9 -DPython_FIND_REGISTRY:STRING=NEVER -DPython_NumPy_INCLUDE_DIRS:PATH=/usr/local/lib/python3.9/site-packages/numpy/core/include -DPython3_EXECUTABLE:PATH=/usr/local/bin/python3.9 -DPython3_ROOT_DIR:PATH=/usr/local -DPython3_INCLUDE_DIR:PATH=/usr/local/include/python3.9 -DPython3_FIND_REGISTRY:STRING=NEVER
-DPython3_NumPy_INCLUDE_DIRS:PATH=/usr/local/lib/python3.9/site-packages/numpy/core/include -DCMAKE_BUILD_TYPE:STRING=Release
-- The C compiler identification is Clang 14.0.5
-- The CXX compiler identification is Clang 14.0.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PythonInterp: /usr/local/bin/python3.9 (found version "3.9.16")
-- Found PythonLibs: /usr/local/lib/libpython3.9.so (found version "3.9.16")
-- Found NumPy: /usr/local/lib/python3.9/site-packages/numpy/core/include (found version "1.23.5")
-- Found F2PY: /usr/local/bin/f2py3 (found version "1.23.5")
-- F2PY included from: /usr/local/lib/python3.9/site-packages/numpy/f2py/src
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
Python3_EXECUTABLE
Python3_FIND_REGISTRY
Python3_INCLUDE_DIR
Python3_NumPy_INCLUDE_DIRS
Python3_ROOT_DIR
Python_EXECUTABLE
Python_FIND_REGISTRY
Python_INCLUDE_DIR
Python_NumPy_INCLUDE_DIRS
Python_ROOT_DIR
SKBUILD
-- Build files have been written to: /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.0.3/_skbuild/freebsd-14.0-CURRENT-i386-3.9/cmake-build
[ 25%] Building C object CMakeFiles/_f2py_runtime_library.dir/usr/local/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.c.o
In file included from /usr/local/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.c:2:
In file included from /usr/local/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.h:13:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948:
/usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
^
1 warning generated.
[ 50%] Linking C static library lib_f2py_runtime_library.a
[ 50%] Built target _f2py_runtime_library
[ 75%] Generating nleq2.cpython-39.so
running build
running config_cc
INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
INFO: build_src
INFO: building extension "nleq2" sources
creating f2py_build
creating f2py_build/src.freebsd-14.0-CURRENT-i386-3.9
creating f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/pysces
creating f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/pysces/nleq2
INFO: f2py options: []
INFO: f2py: /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.0.3/pysces/nleq2/nleq2.pyf
append_needs: unknown need 'int'
append_needs: unknown need 'double'
append_needs: unknown need 'double'
append_needs: unknown need 'int'
append_needs: unknown need 'int'
append_needs: unknown need 'int'
append_needs: unknown need 'double'
append_needs: unknown need 'double'
append_needs: unknown need 'int'
Reading fortran codes...
Reading file '/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.0.3/pysces/nleq2/nleq2.pyf' (format:free)
Post-processing...
Block: nleq2__user__routines
Block: nleq2_user_interface
Block: fcn
Block: jac
Block: nleq2
Block: nleq2
Block: nleq2
In: /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.0.3/pysces/nleq2/nleq2.pyf:nleq2:nleq2:nleq2
get_useparameters: no module nleq2__user__routines info used by nleq2
Post-processing (stage 2)...
Building modules...
Constructing call-back function "cb_fcn_in_nleq2__user__routines"
def fcn(x,ifail,[n]): return f,ifail
Constructing call-back function "cb_jac_in_nleq2__user__routines"
def jac(x,[n,m1]): return a
Building module "nleq2"...
Generating possibly empty wrappers"
Maybe empty "nleq2-f2pywrappers.f"
Constructing wrapper function "nleq2"...
x,xscal,rtol,iopt,ierr = nleq2(fcn,jac,x,xscal,rtol,iopt,iwk,rwk,[n,liwk,lrwk,fcn_extra_args,jac_extra_args])
Wrote C/API module "nleq2" to file "f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/pysces/nleq2/nleq2module.c"
INFO: adding 'f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/pysces/nleq2/fortranobject.c' to sources.
INFO: adding 'f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/pysces/nleq2' to include_dirs.
creating f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/f2py_build
creating f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/f2py_build/src.freebsd-14.0-CURRENT-i386-3.9
creating f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/pysces
creating f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/pysces/nleq2
copying /usr/local/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.c -> f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/pysces/nleq2
copying /usr/local/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.h -> f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/pysces/nleq2
INFO: adding 'f2py_build/src.freebsd-14.0-CURRENT-i386-3.9/pysces/nleq2/nleq2-f2pywrappers.f' to sources.
INFO: build_src: building npy-pkg config files
/usr/local/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build_ext
INFO: customize UnixCCompiler
Traceback (most recent call last):
File "/usr/local/bin/f2py3", line 33, in <module>
sys.exit(load_entry_point('numpy==1.23.5', 'console_scripts', 'f2py3')())
File "/usr/local/lib/python3.9/site-packages/numpy/f2py/f2py2e.py", line 704, in main
run_compile()
File "/usr/local/lib/python3.9/site-packages/numpy/f2py/f2py2e.py", line 671, in run_compile
setup(ext_modules=[ext])
File "/usr/local/lib/python3.9/site-packages/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
File "/usr/local/lib/python3.9/site-packages/setuptools/__init__.py", line 87, in setup
return distutils.core.setup(**attrs)
File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 177, in setup
return run_commands(dist)
File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 193, in run_commands
dist.run_commands()
File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 968, in run_commands
self.run_command(cmd)
File "/usr/local/lib/python3.9/site-packages/setuptools/dist.py", line 1217, in run_command
super().run_command(command)
File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 987, in run_command
cmd_obj.run()
File "/usr/local/lib/python3.9/site-packages/numpy/distutils/command/build.py", line 62, in run
old_build.run(self)
File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 131, in run
self.run_command(cmd_name)
File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 317, in run_command
self.distribution.run_command(command)
File "/usr/local/lib/python3.9/site-packages/setuptools/dist.py", line 1217, in run_command
super().run_command(command)
File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 987, in run_command
cmd_obj.run()
File "/usr/local/lib/python3.9/site-packages/numpy/distutils/command/build_ext.py", line 139, in run
self.compiler.customize(self.distribution)
File "/usr/local/lib/python3.9/site-packages/numpy/distutils/ccompiler.py", line 89, in <lambda>
m = lambda self, *args, **kw: func(self, *args, **kw)
File "/usr/local/lib/python3.9/site-packages/numpy/distutils/ccompiler.py", line 540, in CCompiler_customize
self.compile([fn], output_dir=tmpdir,
File "/usr/local/lib/python3.9/site-packages/numpy/distutils/ccompiler.py", line 89, in <lambda>
m = lambda self, *args, **kw: func(self, *args, **kw)
File "/usr/local/lib/python3.9/site-packages/numpy/distutils/ccompiler.py", line 272, in CCompiler_compile
jobs = get_num_build_jobs()
File "/usr/local/lib/python3.9/site-packages/numpy/distutils/misc_util.py", line 93, in get_num_build_jobs
cpu_count = len(os.sched_getaffinity(0))
OverflowError: could not allocate a large enough CPU set
*** Error code 1
Stop.
make[3]: stopped in /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.0.3/_skbuild/freebsd-14.0-CURRENT-i386-3.9/cmake-build
*** Error code 1
Stop.
make[2]: stopped in /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.0.3/_skbuild/freebsd-14.0-CURRENT-i386-3.9/cmake-build
*** Error code 1
Stop.
make[1]: stopped in /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.0.3/_skbuild/freebsd-14.0-CURRENT-i386-3.9/cmake-build
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/skbuild/setuptools_wrap.py", line 649, in setup
cmkr.make(make_args, install_target=cmake_install_target, env=env)
File "/usr/local/lib/python3.9/site-packages/skbuild/cmaker.py", line 686, in make
self.make_impl(clargs=clargs, config=config, source_dir=source_dir, install_target=install_target, env=env)
File "/usr/local/lib/python3.9/site-packages/skbuild/cmaker.py", line 717, in make_impl
raise SKBuildError(
An error occurred while building with CMake.
Command:
/usr/local/bin/cmake --build . --target install --config Release --
Install target:
install
Source directory:
/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.0.3
Working directory:
/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.0.3/_skbuild/freebsd-14.0-CURRENT-i386-3.9/cmake-build
Please check the install target is valid and see CMake's output for more information.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/py-PySCeS