[SciPy-User] Scipy test failure when building on Scientific Linux 6.0

Dugan Witherick d.witherick@ucl.ac...
Mon Feb 27 08:47:19 CST 2012


Dear Ralf,

I've attached the build log and test log to this message.  I'm guessing
that mail board will scrub the attachments and replace them with links but
I thought it better to do it this way than fill people's inboxes with long
messages.  Please say if you think it is better to just inline the logs.

Dugan

On 26 February 2012 21:43, Ralf Gommers <ralf.gommers@googlemail.com> wrote:

>
>
> On Fri, Feb 24, 2012 at 12:48 PM, Dugan Witherick <d.witherick@ucl.ac.uk>wrote:
>
>> I'm trying to build numpy (1.6.1) and scipy (0.10.1rc2) on Scientific
>> Linux 6.0.  I've successfully managed to build both packages from source
>> using
>>
>> python setup.py config_fc --fcompiler=gnu95 install
>>
>> but while numpy passes its tests, scipy doesn't:
>>
>> >>> scipy.test()
>> Running unit tests for scipy
>> NumPy version 1.6.1
>> NumPy is installed in /usr/lib64/python2.6/site-packages/numpy
>> SciPy version 0.10.1rc2
>> SciPy is installed in /usr/lib64/python2.6/site-packages/scipy
>> Python version 2.6.6 (r266:84292, May 20 2011, 16:42:11) [GCC 4.4.5
>> 20110214 (Red Hat 4.4.5-6)]
>> nose version 0.10.4
>>
>> ---SKIPPED----
>>
>> ======================================================================
>> ERROR: test_qhull.TestTriangulation.test_pathological
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in
>> runTest
>>     self.test(*self.arg)
>>   File
>> "/usr/lib64/python2.6/site-packages/scipy/spatial/tests/test_qhull.py",
>> line 216, in test_pathological
>>     assert_equal(tri.points[tri.vertices].max(),
>> ValueError: zero-size array to maximum.reduce without identity
>>
>> ======================================================================
>> FAIL: test_interpnd.TestCloughTocher2DInterpolator.test_dense
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in
>> runTest
>>     self.test(*self.arg)
>>   File
>> "/usr/lib64/python2.6/site-packages/scipy/interpolate/tests/test_interpnd.py",
>> line 183, in test_dense
>>     err_msg="Function %d" % j)
>>   File
>> "/usr/lib64/python2.6/site-packages/scipy/interpolate/tests/test_interpnd.py",
>> line 132, in _check_accuracy
>>     assert_allclose(a, b, **kw)
>>   File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line
>> 1168, in assert_allclose
>>     verbose=verbose, header=header)
>>   File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line
>> 605, in assert_array_compare
>>     chk_same_position(x_id, y_id, hasval='nan')
>>   File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line
>> 588, in chk_same_position
>>     raise AssertionError(msg)
>> AssertionError:
>> Not equal to tolerance rtol=0.01, atol=0.005
>> Function 0
>> x and y nan location mismatch:
>>  x: array([ nan,  nan,  nan,  nan,  nan,  nan,  nan,  nan,  nan,  nan,
>>  nan,
>>         nan,  nan,  nan,  nan,  nan,  nan,  nan,  nan,  nan,  nan,  nan,
>>         nan,  nan,  nan,  nan,  nan,  nan,  nan,  nan,  nan,  nan,
>>  nan,...
>>  y: array([  3.66796999e-02,   1.91605573e-01,   6.08362261e-01,
>>          7.64324844e-02,   9.18031021e-01,   1.28033199e-01,
>>          4.67121584e-01,   1.37085621e-01,   2.53092671e-01,...
>>
>> ---SKIPPED several other fails---
>>
>> ----------------------------------------------------------------------
>> Ran 5102 tests in 80.529s
>>
>> FAILED (KNOWNFAIL=13, SKIP=35, errors=1, failures=19)
>> <nose.result.TextTestResult run=5102 errors=1 failures=19>
>>
>> numpy/scipy are being built against lapack (3.2.1), blas (3.2.1) and
>> atlas (3.8.3) from the standard Scientific Linux repository.  I would
>> appreciate any advice/suggestions on where I might be going wrong.
>>
>
> Could you post all the test failures and the build log?
>
> Ralf
>
>
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