scipy.test() failure

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scipy.test() failure

Warren Weckesser-2
Hello once again,

A reminder of the facts: Mac OSX 10.4 PPC, gcc 4.0.1 (Apple), gfortran 4.2.1,
numpy-1.0.4 installed.  I am installing scipy-0.6.0.

I built scipy-0.6.0, and I just ran scipy.test().  I get many warnings and
two failures.  A transcript of running scipy.test(1,10) is attached.

Here are the failures:

<quote>
======================================================================
FAIL: check loadmat case sparse
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/wweckesser/test_install/lib/python2.5/site-packages/scipy/io/tests/test_mio.py", line 85, in cc
    self._check_case(name, files, expected)
  File "/Users/wweckesser/test_install/lib/python2.5/site-packages/scipy/io/tests/test_mio.py", line 80, in _check_case
    self._check_level(k_label, expected, matdict[k])
  File "/Users/wweckesser/test_install/lib/python2.5/site-packages/scipy/io/tests/test_mio.py", line 63, in _check_level
    decimal = 5)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py", line 232, in assert_array_almost_
equal
    header='Arrays are not almost equal')
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py", line 217, in assert_array_compare
    assert cond, msg
AssertionError:
Arrays are not almost equal
test sparse; file /Users/wweckesser/test_install/lib/python2.5/site-packages/scipy/io/tests/./data/testsparse_6.5.1_GLNX86.mat, variable testspa
rse
(mismatch 46.6666666667%)
 x: array([[  3.03865194e-319,   3.16202013e-322,   1.04346664e-320,
          2.05531309e-320,   2.56123631e-320],
       [  3.16202013e-322,   0.00000000e+000,   0.00000000e+000,...
 y: array([[ 1.,  2.,  3.,  4.,  5.],
       [ 2.,  0.,  0.,  0.,  0.],
       [ 3.,  0.,  0.,  0.,  0.]])

======================================================================
FAIL: check_dot (scipy.lib.tests.test_blas.test_fblas1_simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/wweckesser/test_install/lib/python2.5/site-packages/scipy/lib/blas/tests/test_blas.py", line 76, in check_dot
    assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py", line 158, in assert_almost_equal
    assert round(abs(desired - actual),decimal) == 0, msg
AssertionError:
Items are not equal:
 ACTUAL: (-1.9987702369689941+4.6526445226967791e-37j)
 DESIRED: (-9+2j)

----------------------------------------------------------------------
</quote>

I found this: http://projects.scipy.org/scipy/scipy/ticket/238
The second failure that I get looks like the same one in that ticket.

Any help is appreciated.

Warren



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Re: scipy.test() failure

Robert Kern-2
On Wed, Apr 16, 2008 at 8:24 PM, Warren Weckesser
<[hidden email]> wrote:

> Hello once again,
>
> A reminder of the facts: Mac OSX 10.4 PPC, gcc 4.0.1 (Apple), gfortran
> 4.2.1,
> numpy-1.0.4 installed.  I am installing scipy-0.6.0.
>
> I built scipy-0.6.0, and I just ran scipy.test().  I get many warnings and
>  two failures.  A transcript of running scipy.test(1,10) is attached.
>
> Here are the failures:
>
> <quote>
> ======================================================================
> FAIL: check loadmat case sparse
>  ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/Users/wweckesser/test_install/lib/python2.5/site-packages/scipy/io/tests/test_mio.py",
> line 85, in cc
>      self._check_case(name, files, expected)
>   File
> "/Users/wweckesser/test_install/lib/python2.5/site-packages/scipy/io/tests/test_mio.py",
> line 80, in _check_case
>     self._check_level(k_label, expected, matdict[k])
>    File
> "/Users/wweckesser/test_install/lib/python2.5/site-packages/scipy/io/tests/test_mio.py",
> line 63, in _check_level
>     decimal = 5)
>   File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py",
> line 232, in assert_array_almost_
>  equal
>     header='Arrays are not almost equal')
>   File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py",
> line 217, in assert_array_compare
>     assert cond, msg
>  AssertionError:
> Arrays are not almost equal
> test sparse; file
> /Users/wweckesser/test_install/lib/python2.5/site-packages/scipy/io/tests/./data/testsparse_6.5.1_GLNX86.mat,
> variable testspa
> rse
> (mismatch 46.6666666667%)
>   x: array([[  3.03865194e-319,   3.16202013e-322,   1.04346664e-320,
>           2.05531309e-320,   2.56123631e-320],
>        [  3.16202013e-322,   0.00000000e+000,   0.00000000e+000,...
>  y: array([[ 1.,  2.,  3.,  4.,  5.],
>         [ 2.,  0.,  0.,  0.,  0.],
>        [ 3.,  0.,  0.,  0.,  0.]])

This looks like a new endianness problem in the matfile reader.

> ======================================================================
> FAIL: check_dot (scipy.lib.tests.test_blas.test_fblas1_simple)
> ----------------------------------------------------------------------
>  Traceback (most recent call last):
>   File
> "/Users/wweckesser/test_install/lib/python2.5/site-packages/scipy/lib/blas/tests/test_blas.py",
> line 76, in check_dot
>     assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j)
>    File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py",
> line 158, in assert_almost_equal
>     assert round(abs(desired - actual),decimal) == 0, msg
> AssertionError:
>  Items are not equal:
>  ACTUAL: (-1.9987702369689941+4.6526445226967791e-37j)
>  DESIRED: (-9+2j)
>
> ----------------------------------------------------------------------
> </quote>
>
> I found this: http://projects.scipy.org/scipy/scipy/ticket/238
>  The second failure that I get looks like the same one in that ticket.

Yes, it is fixed.

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
 -- Umberto Eco
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Re: scipy.test() failure

Warren Weckesser-2


On Wed, Apr 16, 2008 at 10:19 PM, Robert Kern <[hidden email]> wrote:


> I found this: http://projects.scipy.org/scipy/scipy/ticket/238
>  The second failure that I get looks like the same one in that ticket.

Yes, it is fixed.


How do I get the fix?  (I think the answer will be "Apply the patch"; if so, explicit instructions for how to do that would be great.)

Warren



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Re: scipy.test() failure

Robert Kern-2
On Wed, Apr 16, 2008 at 11:06 PM, Warren Weckesser
<[hidden email]> wrote:
> On Wed, Apr 16, 2008 at 10:19 PM, Robert Kern <[hidden email]> wrote:
> > > I found this: http://projects.scipy.org/scipy/scipy/ticket/238
> > >  The second failure that I get looks like the same one in that ticket.
> >
> > Yes, it is fixed.
>
> How do I get the fix?  (I think the answer will be "Apply the patch"; if so,
> explicit instructions for how to do that would be great.)

Check out the latest code using SVN:

  svn co http://svn.scipy.org/svn/scipy/trunk scipy

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
 -- Umberto Eco
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Re: scipy.test() failure

Warren Weckesser-2


On Thu, Apr 17, 2008 at 12:10 AM, Robert Kern <[hidden email]> wrote:


Check out the latest code using SVN:

 svn co http://svn.scipy.org/svn/scipy/trunk scipy

Does the svn version depend on  the svn version of numpy, or can  I stick with numpy 1.0.4? The comment at http://projects.scipy.org/scipy/scipy/roadmap makes me think I'll need a new numpy, but I'll try 1.0.4 first.

Warren


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Re: scipy.test() failure

Robert Kern-2
On Wed, Apr 16, 2008 at 11:56 PM, Warren Weckesser
<[hidden email]> wrote:
> Does the svn version depend on  the svn version of numpy, or can  I stick
> with numpy 1.0.4? The comment at
> http://projects.scipy.org/scipy/scipy/roadmap makes me think I'll need a new
> numpy, but I'll try 1.0.4 first.

It would be best to use SVN numpy.

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
 -- Umberto Eco
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