Gentoo Logo
Gentoo Spaceship




Note: Due to technical difficulties, the Archives are currently not up to date. GMANE provides an alternative service for most mailing lists.
c.f. bug 424647
List Archive: gentoo-science
Navigation:
Lists: gentoo-science: < Prev By Thread Next > < Prev By Date Next >
Headers:
To: gentoo-science@g.o
From: Steven Trogdon <strogdon@...>
Subject: Re: More than 200 hundred errors in testsuite
Date: Wed, 24 Aug 2011 12:50:06 -0500
On Wed, 24 Aug 2011 18:24:56 +0200
rose@... wrote:

> Hi,
> 
> I installed in the last days sage-4.7.1  with the ebuild from
> sage-on-gentoo overlay on four systems (all x86_64 AMD and INTEL).
> After the installation I run the testsuite:
> 
> cd $(mktemp -d) && sage -testall ,
> 
> which reported that between 200 and 250 tests failed. The resulting
> log files (/home/rose/.sage/tmp/test.log) are between 1.5 and 3.3
> MByte. One of these shorter log files is attached.
> 
> I got the message that one reason for the downgrade to numpy-1.5.1 is  
> bug 371099, i.e. missing clapack_* symbols in scipy-0.9.0, if  
> numpy-1.6.x is used.
> 
> My scipy-0.9.0-r1 was installed with numpy-1.6.1. I tried already to  
> reinstall scipy-0.9.0-r1 (now with numpy-1.5.1), but it fails with:
> 
> ...
> RefactoringTool:  
> /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/setup.py
> /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/io/__init__.py
> /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/io/matlab/mio4.py
> /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/io/matlab/mio5.py
> ...
> /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/ode.py
> /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/quadpack.py
> blas_opt_info:
> blas_mkl_info:
>    libraries mkl,vml,guide not found in /usr/local/lib64
>    libraries mkl,vml,guide not found in /usr/local/lib
>    libraries mkl,vml,guide not found in /usr/lib64
>    libraries mkl,vml,guide not found in /usr/lib
>    NOT AVAILABLE
> 
> atlas_blas_threads_info:
> Setting PTATLAS=ATLAS
> Warning: No configuration returned, assuming  
> unavailable./usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:527:
> UserWarning: Specified path  is invalid.
>    warnings.warn('Specified path %s is invalid.' % d)
>    libraries atlcblas,f77blas,m,atlas not found in /usr/lib64
>    NOT AVAILABLE
> 
> atlas_blas_info:
>    libraries atlcblas,f77blas,m,atlas not found in /usr/lib64
>    NOT AVAILABLE
> 
> /usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:1399:  
> 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__)
> blas_info:
>    libraries blas not found in /usr/local/lib64
>    libraries blas not found in /usr/local/lib
>    libraries blas not found in /usr/lib64
>    libraries blas not found in /usr/lib
>    NOT AVAILABLE
> 
> /usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:1408:  
> 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__)
> blas_src_info:
>    NOT AVAILABLE
> 
> /usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:1411:  
> 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 181, in <module>
>      setup_package()
>    File "setup.py", line 173, in setup_package
>      configuration=configuration )
>    File "/usr/lib64/python3.2/site-packages/numpy/distutils/core.py",  
> line 152, in setup
>      config = configuration()
> ...
>    File  
> "/usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py",  
> line 461, 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-0.9.0-r1 failed (compile phase):
>   *   Building failed with CPython 3.2 in distutils_building() function
> 
> 
> Any hint?

A lot of your testsuite failures are scipy/numpy related. The above failure
seems to be from building against the python:3.2 slot. I'm not sure this can be
done? To build scipy against just the python:2.7 slot (this is needed by sog)
do 

USE_PYTHON="2.7" emerge scipy

Hopefully this will get you rolling.
Attachment:
signature.asc (PGP signature)
References:
More than 200 hundred errors in testsuite
-- rose
Navigation:
Lists: gentoo-science: < Prev By Thread Next > < Prev By Date Next >
Previous by thread:
More than 200 hundred errors in testsuite
Next by thread:
flexdock-0.5.2 cannot be downloaded
Previous by date:
More than 200 hundred errors in testsuite
Next by date:
Re: sci-mathematics/sage-4.7.1 and numpy version


Updated Jul 05, 2012

Summary: Archive of the gentoo-science mailing list.

Donate to support our development efforts.

Copyright 2001-2013 Gentoo Foundation, Inc. Questions, Comments? Contact us.