Re: [gentoo-science] Trouble building scipy-0.14.0 against acml

[François Bissey]

You obviously didn't read my last two emails.

Francois

On Sun, 15 Jun 2014 16:22:43 Bastian Löffler wrote:
> I still have this problem when updating to scipy-0.14.0. Ideas?
>
> Am 09.06.2014 20:41, schrieb Bastian Löffler:
> > Hi,
> >
> > this is
> >
> > /var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python2_7/site.cf
> > g:
> >
> > [blas]
> > include_dirs =
> > library_dirs = :/usr/lib64
> > blas_libs =
> > [lapack]
> > library_dirs = //opt/acml5.3.1/gfortran64/lib:/usr/lib64
> > lapack_libs = acml
> >
> > Buliding numpy is ago. This is any scipy update.
> >
> > Am 09.06.2014 13:51, schrieb François Bissey:
> >> numpy not bumpy. Sorry for the noise.
> >>
> >> On 9/06/2014, at 23:42, François Bissey <frp.bissey@×××××.com> wrote:
> >>> Hi,
> >>>
> >>> Could you post the file:
> >>> /var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python2_7/site.
> >>> cfg
> >>> for our perusal? You obviously managed to merge bumpy which
> >>> fundamentally
> >>> should have the exact same problem.
> >>> Was it just before scipy or a while ago?
> >>>
> >>> François
> >>>
> >>> On 9/06/2014, at 23:25, Bastian Löffler <Bastian_Loeffler@×××××.de>
wrote:
> >>>> Hi all,
> >>>>
> >>>> I can not build scipy 0.14.0 agaonst the currenct aclm since it
> >>>> complains a missing blas:
> >>>>
> >>>> numpy.distutils.system_info.BlasNotFoundError:
> >>>>    Blas (
> >>>>
> >>>> http://www.netlib.org/blas/
> >>>> ) libraries not found.
> >>>>
> >>>>    Directories to search for the libraries can be specified in the
> >>>>    numpy/distutils/site.cfg file (section [blas]) or by setting
> >>>>    the BLAS environment variable.
> >>>>
> >>>> * ERROR: sci-libs/scipy-0.14.0::gentoo failed (compile phase):
> >>>> *   (no error message)
> >>>> *
> >>>> * Call stack:
> >>>> *     ebuild.sh, line   93:  Called src_compile
> >>>> *   environment, line 4075:  Called distutils-r1_src_compile
> >>>> *   environment, line 1421:  Called _distutils-r1_run_foreach_impl
> >>>> 'python_compile'
> >>>> *   environment, line  312:  Called python_parallel_foreach_impl
> >>>> 'distutils-r1_run_phase' 'python_compile'
> >>>> *   environment, line 3808:  Called multibuild_parallel_foreach_variant
> >>>> '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
> >>>> *   environment, line 2855:  Called multibuild_foreach_variant
> >>>> '_multibuild_parallel' '_python_multibuild_wrapper'
> >>>> 'distutils-r1_run_phase' 'python_compile'
> >>>> *   environment, line 2798:  Called _multibuild_run
> >>>> '_multibuild_parallel' '_python_multibuild_wrapper'
> >>>> 'distutils-r1_run_phase' 'python_compile'
> >>>> *   environment, line 2796:  Called _multibuild_parallel
> >>>> '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
> >>>> *   environment, line 2846:  Called _python_multibuild_wrapper
> >>>> 'distutils-r1_run_phase' 'python_compile'
> >>>> *   environment, line  914:  Called distutils-r1_run_phase
> >>>> 'python_compile'
> >>>> *   environment, line 1412:  Called python_compile
> >>>> *   environment, line 3315:  Called distutils-r1_python_compile
> >>>> 'config_fc' '--noopt' '--noarch'
> >>>> *   environment, line 1292:  Called esetup.py 'build' 'config_fc'
> >>>> '--noopt' '--noarch'
> >>>> *   environment, line 1862:  Called die
> >>>> * The specific snippet of code:
> >>>> *       "${@}" || die
> >>>> *
> >>>> * If you need support, post the output of `emerge --info
> >>>> '=sci-libs/scipy-0.14.0::gentoo'`,
> >>>> * the complete build log and the output of `emerge -pqv
> >>>> '=sci-libs/scipy-0.14.0::gentoo'`.
> >>>> * The complete build log is located at
> >>>> '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/build.log'.
> >>>> * The ebuild environment file is located at
> >>>> '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/environment'.
> >>>> * Working directory:
> >>>> '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python2_7'
> >>>> * S: '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0'
> >>>> /usr/lib64/portage/bin/isolated-functions.sh: line 226: kill: (6675) -
> >>>> No such process
> >>>> blas_opt_info:
> >>>>
> >>>> system_info:
> >>>>  NOT AVAILABLE
> >>>>
> >>>> blas_info:
> >>>>  libraries  not found in ['/usr/lib64']
> >>>>  NOT AVAILABLE
> >>>>
> >>>> blas_src_info:
> >>>>  NOT AVAILABLE
> >>>>
> >>>> /usr/lib64/python3.3/distutils/dist.py:258: UserWarning: Unknown
> >>>> distribution option: 'test_suite'
> >>>>
> >>>>  warnings.warn(msg)
> >>>>
> >>>> /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py:1511:
> >>>>
> >>>> UserWarning:
> >>>>    Atlas (
> >>>>
> >>>> http://math-atlas.sourceforge.net/
> >>>> ) libraries not found.
> >>>>
> >>>>    Directories to search for the libraries can be specified in the
> >>>>    numpy/distutils/site.cfg file (section [atlas]) or by setting
> >>>>    the ATLAS environment variable.
> >>>>
> >>>>  warnings.warn(AtlasNotFoundError.__doc__)
> >>>>
> >>>> /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py:566:
> >>>> UserWarning: Specified path  is invalid.
> >>>>
> >>>>  warnings.warn('Specified path %s is invalid.' % d)
> >>>>
> >>>> /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py:1520:
> >>>>
> >>>> UserWarning:
> >>>>    Blas (
> >>>>
> >>>> http://www.netlib.org/blas/
> >>>> ) libraries not found.
> >>>>
> >>>>    Directories to search for the libraries can be specified in the
> >>>>    numpy/distutils/site.cfg file (section [blas]) or by setting
> >>>>    the BLAS environment variable.
> >>>>
> >>>>  warnings.warn(BlasNotFoundError.__doc__)
> >>>>
> >>>> /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py:1523:
> >>>>
> >>>> UserWarning:
> >>>>    Blas (
> >>>>
> >>>> http://www.netlib.org/blas/
> >>>> ) sources not found.
> >>>>
> >>>>    Directories to search for the sources can be specified in the
> >>>>    numpy/distutils/site.cfg file (section [blas_src]) or by setting
> >>>>    the BLAS_SRC environment variable.
> >>>>
> >>>>  warnings.warn(BlasSrcNotFoundError.__doc__)
> >>>>
> >>>> Traceback (most recent call last):
> >>>>  File "setup.py", line 237, in <module>
> >>>>
> >>>>    setup_package()
> >>>>
> >>>>  File "setup.py", line 234, in setup_package
> >>>>
> >>>>    setup(**metadata)
> >>>>
> >>>>  File "/usr/lib64/python3.3/site-packages/numpy/distutils/core.py",
> >>>>
> >>>> line 135, in setup
> >>>>
> >>>>    config = configuration()
> >>>>
> >>>>  File "setup.py", line 173, in configuration
> >>>>
> >>>>    config.add_subpackage('scipy')
> >>>>
> >>>>  File
> >>>>
> >>>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py", line
> >>>> 966, in add_subpackage
> >>>>
> >>>>    caller_level = 2)
> >>>>
> >>>>  File
> >>>>
> >>>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py", line
> >>>> 935, in get_subpackage
> >>>>
> >>>>    caller_level = caller_level + 1)
> >>>>
> >>>>  File
> >>>>
> >>>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py", line
> >>>> 872, in _get_configuration_from_setup_py
> >>>>
> >>>>    config = setup_module.configuration(*args)
> >>>>
> >>>>  File "scipy/setup.py", line 12, in configuration
> >>>>
> >>>>    config.add_subpackage('integrate')
> >>>>
> >>>>  File
> >>>>
> >>>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py", line
> >>>> 966, in add_subpackage
> >>>>
> >>>>    caller_level = 2)
> >>>>
> >>>>  File
> >>>>
> >>>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py", line
> >>>> 935, in get_subpackage
> >>>>
> >>>>    caller_level = caller_level + 1)
> >>>>
> >>>>  File
> >>>>
> >>>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py", line
> >>>> 872, in _get_configuration_from_setup_py
> >>>>
> >>>>    config = setup_module.configuration(*args)
> >>>>
> >>>>  File "scipy/integrate/setup.py", line 12, in configuration
> >>>>
> >>>>    blas_opt = get_info('blas_opt',notfound_action=2)
> >>>>
> >>>>  File
> >>>>
> >>>> "/usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py",
> >>>> line 340, in get_info
> >>>>
> >>>>    return cl().get_info(notfound_action)
> >>>>
> >>>>  File
> >>>>
> >>>> "/usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py",
> >>>> line 499, in get_info
> >>>>
> >>>>    raise self.notfounderror(self.notfounderror.__doc__)
> >>>>
> >>>> numpy.distutils.system_info.BlasNotFoundError:
> >>>>    Blas (
> >>>>
> >>>> http://www.netlib.org/blas/
> >>>> ) libraries not found.
> >>>>
> >>>>    Directories to search for the libraries can be specified in the
> >>>>    numpy/distutils/site.cfg file (section [blas]) or by setting
> >>>>    the BLAS environment variable.
> >>>>
> >>>> * ERROR: sci-libs/scipy-0.14.0::gentoo failed (compile phase):
> >>>> *   (no error message)
> >>>> *
> >>>> * Call stack:
> >>>> *     ebuild.sh, line   93:  Called src_compile
> >>>> *   environment, line 4075:  Called distutils-r1_src_compile
> >>>> *   environment, line 1421:  Called _distutils-r1_run_foreach_impl
> >>>> 'python_compile'
> >>>> *   environment, line  312:  Called python_parallel_foreach_impl
> >>>> 'distutils-r1_run_phase' 'python_compile'
> >>>> *   environment, line 3808:  Called multibuild_parallel_foreach_variant
> >>>> '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
> >>>> *   environment, line 2855:  Called multibuild_foreach_variant
> >>>> '_multibuild_parallel' '_python_multibuild_wrapper'
> >>>> 'distutils-r1_run_phase' 'python_compile'
> >>>> *   environment, line 2798:  Called _multibuild_run
> >>>> '_multibuild_parallel' '_python_multibuild_wrapper'
> >>>> 'distutils-r1_run_phase' 'python_compile'
> >>>> *   environment, line 2796:  Called _multibuild_parallel
> >>>> '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
> >>>> *   environment, line 2846:  Called _python_multibuild_wrapper
> >>>> 'distutils-r1_run_phase' 'python_compile'
> >>>> *   environment, line  914:  Called distutils-r1_run_phase
> >>>> 'python_compile'
> >>>> *   environment, line 1412:  Called python_compile
> >>>> *   environment, line 3315:  Called distutils-r1_python_compile
> >>>> 'config_fc' '--noopt' '--noarch'
> >>>> *   environment, line 1292:  Called esetup.py 'build' 'config_fc'
> >>>> '--noopt' '--noarch'
> >>>> *   environment, line 1862:  Called die
> >>>> * The specific snippet of code:
> >>>> *       "${@}" || die
> >>>> *
> >>>> * If you need support, post the output of `emerge --info
> >>>> '=sci-libs/scipy-0.14.0::gentoo'`,
> >>>> * the complete build log and the output of `emerge -pqv
> >>>> '=sci-libs/scipy-0.14.0::gentoo'`.
> >>>> * The complete build log is located at
> >>>> '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/build.log'.
> >>>> * The ebuild environment file is located at
> >>>> '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/environment'.
> >>>> * Working directory:
> >>>> '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python3_3'
> >>>> * S: '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0'
> >>>> /usr/lib64/portage/bin/isolated-functions.sh: line 226: kill: (6675) -
> >>>> No such process
> >>>>
> >>>>>>> Failed to emerge sci-libs/scipy-0.14.0, Log file: