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

Ralf Gommers ralf.gommers@googlemail....
Sun Feb 26 15:43:27 CST 2012


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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