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

Ralf Gommers ralf.gommers@googlemail....
Tue Feb 28 15:29:13 CST 2012


On Mon, Feb 27, 2012 at 3:47 PM, Dugan Witherick <d.witherick@ucl.ac.uk>wrote:

> 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.
>

This worked fine. The build log is certainly too long to put in a mail.

All the test failures come from the interpolate module. There are some
warnings like
     warning: "_POSIX_C_SOURCE" redefined
which I don't think hurt too much, but indicate something unusual about
your setup.

There's a bunch more that looks wrong, but I have no idea about the cause:

compile options: '-I/usr/lib64/python2.6/site-packages/numpy/core/include
-I/usr/include/python2.6 -c'
gcc: scipy/interpolate/interpnd.c
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1532:
warning: ‘_import_array’ defined but not used
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__ufunc_api.h:226:
warning: ‘_import_umath’ defined but not used
scipy/interpolate/interpnd.c: In function
‘__pyx_f_8interpnd__clough_tocher_2d_single_double’:
scipy/interpolate/interpnd.c:4383: warning: ‘__pyx_v_g1’ may be used
uninitialized in this function
scipy/interpolate/interpnd.c:4384: warning: ‘__pyx_v_g2’ may be used
uninitialized in this function
scipy/interpolate/interpnd.c:4385: warning: ‘__pyx_v_g3’ may be used
uninitialized in this function
scipy/interpolate/interpnd.c: In function
‘__pyx_f_8interpnd__clough_tocher_2d_single_complex’:
scipy/interpolate/interpnd.c:4683: warning: ‘__pyx_v_g1’ may be used
uninitialized in this function
scipy/interpolate/interpnd.c:4684: warning: ‘__pyx_v_g2’ may be used
uninitialized in this function
scipy/interpolate/interpnd.c:4685: warning: ‘__pyx_v_g3’ may be used
uninitialized in this function
gcc -pthread -shared
build/temp.linux-x86_64-2.6/scipy/interpolate/interpnd.o -L/usr/lib64
-Lbuild/temp.linux-x86_64-2.6 -lpython2.6 -o
build/lib.linux-x86_64-2.6/scipy/interpolate/interpnd.so
building 'scipy.interpolate._fitpack' extension
compiling C sources
C compiler: gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv
-DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fwrapv -fPIC

creating build/temp.linux-x86_64-2.6/scipy/interpolate/src
compile options: '-I/usr/lib64/python2.6/site-packages/numpy/core/include
-I/usr/include/python2.6 -c'
gcc: scipy/interpolate/src/_fitpackmodule.c
In file included from scipy/interpolate/src/_fitpackmodule.c:7:
scipy/interpolate/src/__fitpack.h: In function ‘fitpack_surfit’:
scipy/interpolate/src/__fitpack.h:272: warning: passing argument 18 of
‘surfit_’ from incompatible pointer type
scipy/interpolate/src/__fitpack.h:97: note: expected ‘int *’ but argument
is of type ‘npy_intp *’
scipy/interpolate/src/__fitpack.h:272: warning: passing argument 20 of
‘surfit_’ from incompatible pointer type
scipy/interpolate/src/__fitpack.h:97: note: expected ‘int *’ but argument
is of type ‘npy_intp *’
scipy/interpolate/src/__fitpack.h:282: warning: passing argument 18 of
‘surfit_’ from incompatible pointer type
scipy/interpolate/src/__fitpack.h:97: note: expected ‘int *’ but argument
is of type ‘npy_intp *’
scipy/interpolate/src/__fitpack.h:282: warning: passing argument 20 of
‘surfit_’ from incompatible pointer type
scipy/interpolate/src/__fitpack.h:97: note: expected ‘int *’ but argument
is of type ‘npy_intp *’
scipy/interpolate/src/__fitpack.h: In function ‘fitpack_parcur’:

Ralf




> 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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>>
>
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