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
1 On Wed, 24 Aug 2011 18:24:56 +0200
2 rose@××××××××××××××.de wrote:
3
4 > Hi,
5 >
6 > I installed in the last days sage-4.7.1 with the ebuild from
7 > sage-on-gentoo overlay on four systems (all x86_64 AMD and INTEL).
8 > After the installation I run the testsuite:
9 >
10 > cd $(mktemp -d) && sage -testall ,
11 >
12 > which reported that between 200 and 250 tests failed. The resulting
13 > log files (/home/rose/.sage/tmp/test.log) are between 1.5 and 3.3
14 > MByte. One of these shorter log files is attached.
15 >
16 > I got the message that one reason for the downgrade to numpy-1.5.1 is
17 > bug 371099, i.e. missing clapack_* symbols in scipy-0.9.0, if
18 > numpy-1.6.x is used.
19 >
20 > My scipy-0.9.0-r1 was installed with numpy-1.6.1. I tried already to
21 > reinstall scipy-0.9.0-r1 (now with numpy-1.5.1), but it fails with:
22 >
23 > ...
24 > RefactoringTool:
25 > /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/setup.py
26 > /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/io/__init__.py
27 > /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/io/matlab/mio4.py
28 > /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/io/matlab/mio5.py
29 > ...
30 > /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/ode.py
31 > /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/quadpack.py
32 > blas_opt_info:
33 > blas_mkl_info:
34 > libraries mkl,vml,guide not found in /usr/local/lib64
35 > libraries mkl,vml,guide not found in /usr/local/lib
36 > libraries mkl,vml,guide not found in /usr/lib64
37 > libraries mkl,vml,guide not found in /usr/lib
38 > NOT AVAILABLE
39 >
40 > atlas_blas_threads_info:
41 > Setting PTATLAS=ATLAS
42 > Warning: No configuration returned, assuming
43 > unavailable./usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:527:
44 > UserWarning: Specified path is invalid.
45 > warnings.warn('Specified path %s is invalid.' % d)
46 > libraries atlcblas,f77blas,m,atlas not found in /usr/lib64
47 > NOT AVAILABLE
48 >
49 > atlas_blas_info:
50 > libraries atlcblas,f77blas,m,atlas not found in /usr/lib64
51 > NOT AVAILABLE
52 >
53 > /usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:1399:
54 > UserWarning:
55 > Atlas (http://math-atlas.sourceforge.net/) libraries not found.
56 > Directories to search for the libraries can be specified in the
57 > numpy/distutils/site.cfg file (section [atlas]) or by setting
58 > the ATLAS environment variable.
59 > warnings.warn(AtlasNotFoundError.__doc__)
60 > blas_info:
61 > libraries blas not found in /usr/local/lib64
62 > libraries blas not found in /usr/local/lib
63 > libraries blas not found in /usr/lib64
64 > libraries blas not found in /usr/lib
65 > NOT AVAILABLE
66 >
67 > /usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:1408:
68 > UserWarning:
69 > Blas (http://www.netlib.org/blas/) libraries not found.
70 > Directories to search for the libraries can be specified in the
71 > numpy/distutils/site.cfg file (section [blas]) or by setting
72 > the BLAS environment variable.
73 > warnings.warn(BlasNotFoundError.__doc__)
74 > blas_src_info:
75 > NOT AVAILABLE
76 >
77 > /usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:1411:
78 > UserWarning:
79 > Blas (http://www.netlib.org/blas/) sources not found.
80 > Directories to search for the sources can be specified in the
81 > numpy/distutils/site.cfg file (section [blas_src]) or by setting
82 > the BLAS_SRC environment variable.
83 > warnings.warn(BlasSrcNotFoundError.__doc__)
84 > Traceback (most recent call last):
85 > File "setup.py", line 181, in <module>
86 > setup_package()
87 > File "setup.py", line 173, in setup_package
88 > configuration=configuration )
89 > File "/usr/lib64/python3.2/site-packages/numpy/distutils/core.py",
90 > line 152, in setup
91 > config = configuration()
92 > ...
93 > File
94 > "/usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py",
95 > line 461, in get_info
96 > raise self.notfounderror(self.notfounderror.__doc__)
97 > numpy.distutils.system_info.BlasNotFoundError:
98 > Blas (http://www.netlib.org/blas/) libraries not found.
99 > Directories to search for the libraries can be specified in the
100 > numpy/distutils/site.cfg file (section [blas]) or by setting
101 > the BLAS environment variable.
102 > * ERROR: sci-libs/scipy-0.9.0-r1 failed (compile phase):
103 > * Building failed with CPython 3.2 in distutils_building() function
104 >
105 >
106 > Any hint?
107
108 A lot of your testsuite failures are scipy/numpy related. The above failure
109 seems to be from building against the python:3.2 slot. I'm not sure this can be
110 done? To build scipy against just the python:2.7 slot (this is needed by sog)
111 do
112
113 USE_PYTHON="2.7" emerge scipy
114
115 Hopefully this will get you rolling.

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