[SciPy-User] Scipy test errors

Scott Sinclair scott.sinclair.za@gmail....
Fri Jul 27 04:20:02 CDT 2012


On 26 July 2012 22:13, Johann Rohwer <jr@sun.ac.za> wrote:
> On 26/07/2012 21:57, Ralf Gommers wrote:
>>
>>
>> On Thu, Jul 26, 2012 at 9:51 PM, Johann Rohwer <jr@sun.ac.za
>> <mailto:jr@sun.ac.za>> wrote:
>>
>>     The latest SciPy from GIT gives a whole bunch of test errors and failures,
>>     most of the in the test_arpack module:
>>
>>     Ran 5483 tests in 78.064s
>>
>>     FAILED (KNOWNFAIL=13, SKIP=24, errors=8, failures=63)
>>     Out[4]: <nose.result.TextTestResult run=5483 errors=8 failures=63>
>>
>>     Is this to be expected? The official release 0.11.0rc1 gives slightly fewer,
>>     but still a significant number of failures (57).
>>
>>
>> That's not expected. Could you please send us the output of the test run?
>> And with what command did you install, and what Python version?
>>
>> Ralf
> Test output below, version info included. Installation was with
> $ python setup.py build
> $ sudo python setup.py install
>
> I made sure to clean out the build directory first, and remove any scipy*
> files/dirs from the dist-packages directory.
>
>
> ------------------------ test output below -------------------------------
>
> In [3]: scipy.test()
> Running unit tests for scipy
> NumPy version 1.8.0.dev-b74c6be
> NumPy is installed in /usr/local/lib/python2.7/dist-packages/numpy
> SciPy version 0.12.0.dev-8e918cd
> SciPy is installed in /usr/local/lib/python2.7/dist-packages/scipy
> Python version 2.7.3 (default, Apr 20 2012, 22:39:59) [GCC 4.6.3]
> nose version 1.1.2
> ----------------------------------------------------------------------
> Ran 5483 tests in 76.694s
>
> FAILED (KNOWNFAIL=13, SKIP=24, errors=8, failures=66)
> Out[3]: <nose.result.TextTestResult run=5483 errors=8 failures=66>

On the same platform I see the 8 errors (RuntimeWarning: overflow
encountered in nbdtrik), but none of the failures. Some of the
failures you see might be caused by running the tests multiple times
in the same Python process. What happens if you run the following from
the command line instead of inside an IPython session?

$ python -c "import scipy; scipy.test()"

Here is my test output:


Running unit tests for scipy
NumPy version 1.8.0.dev-b74c6be
NumPy is installed in
/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/numpy
SciPy version 0.12.0.dev-8e918cd
SciPy is installed in
/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy
Python version 2.7.3 (default, Apr 20 2012, 22:39:59) [GCC 4.6.3]
nose version 1.1.2
..............................................................................................................................................................................................................................K........................................................................................................K..................................................................K..K......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSS......SSSSSS......SSSS..............................................................................................................................................................................................................................................................................................................................................................................K.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSSSSSSS.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K..................................................................K................................................................................................................................................................KK.......................................................................................................................................................................................................................................................................................................................................................................................................................................................K.K.............................................................................................................................................................................................................................................................................................................................................................................................K........K..............SSSSSSS..............................................................................................................................EEEE....EEEE..................................S..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.nbinom_gen
object at 0x2740e10>, (5, 0.5), 'nbinom cdf_ppf')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/scott/.local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/tests/test_discrete_basic.py",
line 104, in check_cdf_ppf
    ppf05 = distfn.ppf(0.5,*arg)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6132, in ppf
    place(output,cond,self._ppf(*goodargs) + loc)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6633, in _ppf
    vals = ceil(special.nbdtrik(q,n,p))
RuntimeWarning: overflow encountered in nbdtrik

======================================================================
ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.nbinom_gen
object at 0x2740e10>, (5, 0.5), array([ 0,  1,  2,  3,  4,  5,  6,  7,
 8,  9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21]), 'nbinom
cdf_ppf')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/scott/.local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/tests/test_discrete_basic.py",
line 111, in check_cdf_ppf2
    npt.assert_array_equal(distfn.ppf(distfn.cdf(supp,*arg),*arg),
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6132, in ppf
    place(output,cond,self._ppf(*goodargs) + loc)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6633, in _ppf
    vals = ceil(special.nbdtrik(q,n,p))
RuntimeWarning: overflow encountered in nbdtrik

======================================================================
ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.nbinom_gen
object at 0x2740e10>, (5, 0.5), 'nbinom pmf_cdf')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/scott/.local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/tests/test_discrete_basic.py",
line 136, in check_pmf_cdf
    startind = np.int(distfn._ppf(0.01,*arg)-1)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6633, in _ppf
    vals = ceil(special.nbdtrik(q,n,p))
RuntimeWarning: overflow encountered in nbdtrik

======================================================================
ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.nbinom_gen
object at 0x2740e10>, (5, 0.5), 'nbinom oth')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/scott/.local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/tests/test_discrete_basic.py",
line 156, in check_oth
    median_sf = distfn.isf(0.5, *arg)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6184, in isf
    place(output,cond,self._isf(*goodargs) + loc) #PB same as ticket 766
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 5828, in _isf
    return self._ppf(1-q,*args)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6633, in _ppf
    vals = ceil(special.nbdtrik(q,n,p))
RuntimeWarning: overflow encountered in nbdtrik

======================================================================
ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.nbinom_gen
object at 0x2740e10>, (0.4, 0.4), 'nbinom cdf_ppf')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/scott/.local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/tests/test_discrete_basic.py",
line 104, in check_cdf_ppf
    ppf05 = distfn.ppf(0.5,*arg)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6132, in ppf
    place(output,cond,self._ppf(*goodargs) + loc)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6633, in _ppf
    vals = ceil(special.nbdtrik(q,n,p))
RuntimeWarning: overflow encountered in nbdtrik

======================================================================
ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.nbinom_gen
object at 0x2740e10>, (0.4, 0.4), array([ 0,  1,  2,  3,  4,  5,  6,
7,  8,  9, 10, 12]), 'nbinom cdf_ppf')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/scott/.local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/tests/test_discrete_basic.py",
line 111, in check_cdf_ppf2
    npt.assert_array_equal(distfn.ppf(distfn.cdf(supp,*arg),*arg),
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6132, in ppf
    place(output,cond,self._ppf(*goodargs) + loc)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6633, in _ppf
    vals = ceil(special.nbdtrik(q,n,p))
RuntimeWarning: overflow encountered in nbdtrik

======================================================================
ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.nbinom_gen
object at 0x2740e10>, (0.4, 0.4), 'nbinom pmf_cdf')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/scott/.local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/tests/test_discrete_basic.py",
line 136, in check_pmf_cdf
    startind = np.int(distfn._ppf(0.01,*arg)-1)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6633, in _ppf
    vals = ceil(special.nbdtrik(q,n,p))
RuntimeWarning: overflow encountered in nbdtrik

======================================================================
ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.nbinom_gen
object at 0x2740e10>, (0.4, 0.4), 'nbinom oth')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/scott/.local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/tests/test_discrete_basic.py",
line 156, in check_oth
    median_sf = distfn.isf(0.5, *arg)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6184, in isf
    place(output,cond,self._isf(*goodargs) + loc) #PB same as ticket 766
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 5828, in _isf
    return self._ppf(1-q,*args)
  File "/home/scott/.virtualenvs/scipy-sandbox/local/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 6633, in _ppf
    vals = ceil(special.nbdtrik(q,n,p))
RuntimeWarning: overflow encountered in nbdtrik

----------------------------------------------------------------------
Ran 5483 tests in 54.123s

FAILED (KNOWNFAIL=13, SKIP=35, errors=8)

Cheers,
Scott


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