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

Dugan Witherick d.witherick@ucl.ac...
Fri Feb 24 05:48:46 CST 2012


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.

Thanks,
Dugan
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