Gentoo Archives: gentoo-science

From: Steven Trogdon <strogdon@×××××.edu>
To: gentoo-science@l.g.o
Subject: Re: [gentoo-science] More than 200 hundred errors in testsuite
Date: Wed, 24 Aug 2011 17:51:23
Message-Id: 20110824125006.36425eb0@pavilion64.home.lan
In Reply to: [gentoo-science] More than 200 hundred errors in testsuite by rose@rz.uni-potsdam.de
On Wed, 24 Aug 2011 18:24:56 +0200
rose@××××××××××××××.de 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.

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