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

k0ala k0ala.gmane@augrime....
Tue Nov 8 15:52:21 CST 2011


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)

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.

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@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@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
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----------------------------------------------------------------------
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
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.................................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))
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................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))
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======================================================================
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])

======================================================================
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)

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?

Thanks, best,
k0ala

P.S. I replaced the ">>>" by "->>>" because gmane thought I was "top-posting"...



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