[SciPy-User] scipy 0.9 fails tests in windows XP

Wed Nov 9 02:09:21 EST 2011

On Tue, Nov 8, 2011 at 10:52 PM, k0ala <k0ala.gmane at augrime.net> wrote:

> Dear group,
>
> I am doing a clean install of Windows XP SP3, and I have setup Python 2.7,
> Numpy
> 1.6.1 and Scipy 0.9, all via the standard Windows installers. Python seems
> to
> work well enough.
>
> However, when I follow the recommendations on testing the installations:
> (http://www.scipy.org/FAQ#head-75a5d2cc3678224d8e72fb4f58aa0f0639428722)
>  import numpy
>  numpy.test(level=1)
>  import scipy
>  scipy.test(level=1)
>

Those are old, fixed now.

>
> I run into problems. First, there is an error message that does not
> understand
> the "level=1" argument. When I run numpy.test() -- i.e. without arguments,
> there
> is a longer error: it says I have to install "nose" for tests. This I do
> via
> easy_install, and numpy.test() then terminates with an "OK" ruling.
>
> You did the right things.

> So far so good, but now there is a problem I don't know how to solve.
> Running
> scipy.test() results in two failures. The final lines are:
>
> Ran 4728 tests in 69.475s
> FAILED (KNOWNFAIL=12, SKIP=42, failures=2)
> <nose.result.TextTestResult run=4728 errors=0 failures=2>
>
> I am attaching the output of the session below.
>
>
> Microsoft Windows XP [Version 5.1.2600]
> (C) Copyright 1985-2001 Microsoft Corp.
>
> C:\Documents and Settings\koa>python
> Python 2.7.2 (default, Jun 12 2011, 15:08:59) [MSC v.1500 32 bit (Intel)]
> on win
> 32
> Type "help", "copyright", "credits" or "license" for more information.
> ->>> import numpy
> ->>> numpy.test()
> Running unit tests for numpy
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File "C:\Python27\lib\site-packages\numpy\testing\nosetester.py", line
> 318, in
>  test
>    self._show_system_info()
>  File "C:\Python27\lib\site-packages\numpy\testing\nosetester.py", line
> 187, in
>  _show_system_info
>    nose = import_nose()
>  File "C:\Python27\lib\site-packages\numpy\testing\nosetester.py", line
> 69, in
> import_nose
>    raise ImportError(msg)
> ImportError: Need nose >= 0.10.0 for tests - see
> http://somethingaboutorange.com
> /mrl/projects/nose
> ->>> numpy.test(level=1)
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
> TypeError: test() got an unexpected keyword argument 'level'
> ->>> quit()
>
>
>
> koa at cobila ~
> $ easy_install nose
> Searching for nose
> Reading http://pypi.python.org/simple/nose/
> Reading http://somethingaboutorange.com/mrl/projects/nose/
> Reading http://readthedocs.org/docs/nose/
> Best match: nose 1.1.2
> Downloading
> http://pypi.python.org/packages/source/n/nose/nose-1.1.2.tar.gz#md5=
> 144f237b615e23f21f6a50b2183aa817
> Processing nose-1.1.2.tar.gz
> Running nose-1.1.2\setup.py -q bdist_egg --dist-dir
> c:\cygwin\tmp\easy_install-x
> 0cka7\nose-1.1.2\egg-dist-tmp-rm8rsq
> Adding nose 1.1.2 to easy-install.pth file
> Installing nosetests-script.py script to C:\Python27\Scripts
> Installing nosetests.exe script to C:\Python27\Scripts
> Installing nosetests.exe.manifest script to C:\Python27\Scripts
> Installing nosetests-2.7-script.py script to C:\Python27\Scripts
> Installing nosetests-2.7.exe script to C:\Python27\Scripts
> Installing nosetests-2.7.exe.manifest script to C:\Python27\Scripts
>
> Installed c:\python27\lib\site-packages\nose-1.1.2-py2.7.egg
> Processing dependencies for nose
> Finished processing dependencies for nose
>
>
>
> koa at cobila ~
> $ python
> Python 2.7.2 (default, Jun 12 2011, 15:08:59) [MSC v.1500 32 bit (Intel)]
> on win
> 32
> Type "help", "copyright", "credits" or "license" for more information.
> ->>> import numpy
> ->>> numpy.test(level=1)
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
> TypeError: test() got an unexpected keyword argument 'level'
> ->>> numpy.test()
> Running unit tests for numpy
> NumPy version 1.6.1
> NumPy is installed in C:\Python27\lib\site-packages\numpy
> Python version 2.7.2 (default, Jun 12 2011, 15:08:59) [MSC v.1500 32 bit
> (Intel)
> ]
> nose version 1.1.2
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ..........................................................................K.....
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ......K...............................................................K..K......
>
> ........................K...SK.S.......S........................................
>
> ......................................S.........................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ......................K.........K...............................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ..S.............................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
> ........................................
> ----------------------------------------------------------------------
> Ran 2999 tests in 22.263s
>
> OK (KNOWNFAIL=8, SKIP=5)
> <nose.result.TextTestResult run=2999 errors=0 failures=0>
> ->>> import scipy
> ->>> scipy.test()
> Running unit tests for scipy
> NumPy version 1.6.1
> NumPy is installed in C:\Python27\lib\site-packages\numpy
> SciPy version 0.9.0
> SciPy is installed in C:\Python27\lib\site-packages\scipy
> Python version 2.7.2 (default, Jun 12 2011, 15:08:59) [MSC v.1500 32 bit
> (Intel)
> ]
> nose version 1.1.2
>
> ................................................................................
>
> ................................................................................
>
> .............................................K..................................
>
> ................................................................................
>
> ....K..K........................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ............................................................................SSSS
>
> SS......SSSSSS......SSSS........................................................
>
> .........S.........F............................................................
>
> ................................................................................
>
> ..........................................................K.....................
>
> ................................................................................
>
> ................................................................................
>
> ......SSSSS.........S...........................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ..................................................SSSSSSSSSSS...................
>
> ................................................................................
>
> .............................................................K..................
>
> .............................................K..................................
>
> ................................................................................
>
> .........................................KK.....................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> .................................C:\Python27\lib\site-packages\scipy\special\tes
> ts\test_basic.py:1589: RuntimeWarning: invalid value encountered in
> absolute
>  assert_(np.abs(c2) >= 1e300, (v, z))
>
> .........................K.K....................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ....K........K.........SSSSSSS..................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................C:\Python27\lib\site-packages\scipy\stats\distributions.py:3546:
>  RuntimeWarning: overflow encountered in exp
>  return exp(c*x-exp(x)-gamln(c))
>
> .................................C:\Python27\lib\site-packages\scipy\stats\distr
> ibutions.py:3955: RuntimeWarning: invalid value encountered in sqrt
>  vals = 2*(bt+1.0)*sqrt(b-2.0)/((b-3.0)*sqrt(b))
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> .........................................................S......................
>
> ................................................................................
>
> ................................................................................
>
> ........F.......................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
>
> ................................................................................
> ......
> ======================================================================
> FAIL: Test singular pair
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "C:\Python27\lib\site-packages\nose-1.1.2-py2.7.egg\nose\case.py",
> line 1
> 97, in runTest
>    self.test(*self.arg)
>  File "C:\Python27\lib\site-packages\scipy\linalg\tests\test_decomp.py",
> line 2
> 02, in test_singular
>    self._check_gen_eig(A, B)
>  File "C:\Python27\lib\site-packages\scipy\linalg\tests\test_decomp.py",
> line 1
> 89, in _check_gen_eig
>    err_msg=msg)
>  File "C:\Python27\lib\site-packages\numpy\testing\utils.py", line 800, in
> asse
> rt_array_almost_equal
>    header=('Arrays are not almost equal to %d decimals' % decimal))
>  File "C:\Python27\lib\site-packages\numpy\testing\utils.py", line 636, in
> asse
> rt_array_compare
>    raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal to 6 decimals
>
> array([[22, 34, 31, 31, 17],
>       [45, 45, 42, 19, 29],
>       [39, 47, 49, 26, 34],
>       [27, 31, 26, 21, 15],
>       [38, 44, 44, 24, 30]])
> array([[13, 26, 25, 17, 24],
>       [31, 46, 40, 26, 37],
>       [26, 40, 19, 25, 25],
>       [16, 25, 27, 14, 23],
>       [24, 35, 18, 21, 22]])
> (mismatch 25.0%)
>  x: array([ -2.45037885e-01 +0.00000000e+00j,
>         5.17637463e-16 -4.01120590e-08j,
>         5.17637463e-16 +4.01120590e-08j,   2.00000000e+00
> +0.00000000e+00j])
>  y: array([ -3.74550285e-01 +0.00000000e+00j,
>        -5.17716907e-17 -1.15230800e-08j,
>        -5.17716907e-17 +1.15230800e-08j,   2.00000000e+00
> +0.00000000e+00j])
>
>
This one can't be reproduced on most other systems, it may have something
to do with your ATLAS or hardware. See
http://mail.scipy.org/pipermail/scipy-dev/2011-January/015868.html

======================================================================
> FAIL: test_expon (test_morestats.TestAnderson)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "C:\Python27\lib\site-packages\scipy\stats\tests\test_morestats.py",
> line
>  72, in test_expon
>    assert_array_less(crit[:-1], A)
>  File "C:\Python27\lib\site-packages\numpy\testing\utils.py", line 869, in
> asse
> rt_array_less
>    header='Arrays are not less-ordered')
>  File "C:\Python27\lib\site-packages\numpy\testing\utils.py", line 613, in
> asse
> rt_array_compare
>    chk_same_position(x_id, y_id, hasval='inf')
>  File "C:\Python27\lib\site-packages\numpy\testing\utils.py", line 588, in
> chk_
> same_position
>    raise AssertionError(msg)
> AssertionError:
> Arrays are not less-ordered
>
> x and y inf location mismatch:
>  x: array([ 0.911,  1.065,  1.325,  1.587])
>  y: array(inf)
>
> This is only a problem in the test, not with the functionality. It has
been corrected for the next scipy release.

> Ran 4728 tests in 69.475s
>
> FAILED (KNOWNFAIL=12, SKIP=42, failures=2)
> <nose.result.TextTestResult run=4728 errors=0 failures=2>
>
>
> Is this going to be a problem for using scipy? Do you have any
> recommendations
> for getting it to work, or for doing a cleaner install?
>
> That one failure isn't likely to give you problems. If you want to
investigate anyway, you can start with checking the questions by Pauli in
the thread I linked to.

Cheers,
Ralf
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20111109/0cd25c43/attachment.html>