[SciPy-user] Running scipy.test on recent SVN build
Joshua Lippai
discerptor at gmail.com
Fri Mar 21 19:58:31 EDT 2008
Alright, I tried running it without any argument in the parentheses,
and tests run, but with a failure and lots of errors.
>>> scipy.test()
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linsolve/__init__.py:4:
DeprecationWarning: scipy.linsolve has moved to
scipy.sparse.linalg.dsolve
warn('scipy.linsolve has moved to scipy.sparse.linalg.dsolve',
DeprecationWarning)
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/splinalg/__init__.py:3:
DeprecationWarning: scipy.splinalg has moved to scipy.sparse.linalg
warn('scipy.splinalg has moved to scipy.sparse.linalg', DeprecationWarning)
.../Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/vq.py:477:
UserWarning: One of the clusters is empty. Re-run kmean with a
different initialization.
warnings.warn("One of the clusters is empty. "
exception raised as expected: One of the clusters is empty. Re-run
kmean with a different initialization.
................................................................/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/interpolate/fitpack2.py:458:
UserWarning:
The coefficients of the spline returned have been computed as the
minimal norm least-squares solution of a (numerically) rank deficient
system (deficiency=7). If deficiency is large, the results may be
inaccurate. Deficiency may strongly depend on the value of eps.
warnings.warn(message)
...........................................
Don't worry about a warning regarding the number of bytes read.
Warning: 1000000 bytes requested, 20 bytes read.
./Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/utils.py:111:
DeprecationWarning: write_array is deprecated
warnings.warn(str1, DeprecationWarning)
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/utils.py:111:
DeprecationWarning: read_array is deprecated
warnings.warn(str1, DeprecationWarning)
..................../Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/utils.py:111:
DeprecationWarning: npfile is deprecated
warnings.warn(str1, DeprecationWarning)
............................caxpy:n=4
..caxpy:n=3
....ccopy:n=4
..ccopy:n=3
.............cscal:n=4
....cswap:n=4
..cswap:n=3
.....daxpy:n=4
..daxpy:n=3
....dcopy:n=4
..dcopy:n=3
.............dscal:n=4
....dswap:n=4
..dswap:n=3
.....saxpy:n=4
..saxpy:n=3
....scopy:n=4
..scopy:n=3
.............sscal:n=4
....sswap:n=4
..sswap:n=3
.....zaxpy:n=4
..zaxpy:n=3
....zcopy:n=4
..zcopy:n=3
.............zscal:n=4
....zswap:n=4
..zswap:n=3
..
****************************************************************
WARNING: clapack module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
then scipy uses flapack instead of clapack.
****************************************************************
..........................................NO ATLAS INFO AVAILABLE
.........................................
****************************************************************
WARNING: cblas module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
then scipy uses fblas instead of cblas.
****************************************************************
...............................................................................................caxpy:n=4
..caxpy:n=3
....ccopy:n=4
..ccopy:n=3
.............cscal:n=4
....cswap:n=4
..cswap:n=3
.....daxpy:n=4
..daxpy:n=3
....dcopy:n=4
..dcopy:n=3
.............dscal:n=4
....dswap:n=4
..dswap:n=3
.....saxpy:n=4
..saxpy:n=3
....scopy:n=4
..scopy:n=3
.............sscal:n=4
....sswap:n=4
..sswap:n=3
.....zaxpy:n=4
..zaxpy:n=3
....zcopy:n=4
..zcopy:n=3
.............zscal:n=4
....zswap:n=4
..zswap:n=3
....
****************************************************************
WARNING: clapack module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
then scipy uses flapack instead of clapack.
****************************************************************
...Result may be inaccurate, approximate err = 1.23518201169e-08
...Result may be inaccurate, approximate err = 7.27595761418e-12
.....SSS........................................................................................................................................................................................................................................................................................................................................................................................................./Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/ndimage/_segmenter.py:35:
UserWarning: The segmentation code is under heavy development and
therefore the public API will change in the future. The NIPY group is
actively working on this code, and has every intention of generalizing
this for the Scipy community. Use this module minimally, if at all,
until it this warning is removed.
warnings.warn(_msg, UserWarning)
EEE............................................SSSSSSSSSSS.....
_naupd: Number of update iterations taken
-----------------------------------------
1 - 1: 12
_naupd: Number of wanted "converged" Ritz values
------------------------------------------------
1 - 1: 4
_naupd: Real part of the final Ritz values
------------------------------------------
1 - 4: 1.033D+00 7.746D-01 5.164D-01 2.582D-01
_naupd: Imaginary part of the final Ritz values
-----------------------------------------------
1 - 4: 0.000D+00 0.000D+00 0.000D+00 0.000D+00
_naupd: Associated Ritz estimates
---------------------------------
1 - 4: 3.197D-15 3.493D-18 2.179D-23 2.140D-26
=============================================
= Nonsymmetric implicit Arnoldi update code =
= Version Number: 2.4 =
= Version Date: 07/31/96 =
=============================================
= Summary of timing statistics =
=============================================
Total number update iterations = 12
Total number of OP*x operations = 55
Total number of B*x operations = 0
Total number of reorthogonalization steps = 54
Total number of iterative refinement steps = 0
Total number of restart steps = 0
Total time in user OP*x operation = 0.001100
Total time in user B*x operation = 0.000000
Total time in Arnoldi update routine = 0.002971
Total time in naup2 routine = 0.002768
Total time in basic Arnoldi iteration loop = 0.001710
Total time in reorthogonalization phase = 0.000257
Total time in (re)start vector generation = 0.000004
Total time in Hessenberg eig. subproblem = 0.000693
Total time in getting the shifts = 0.000045
Total time in applying the shifts = 0.000210
Total time in convergence testing = 0.000023
Total time in computing final Ritz vectors = 0.000000
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................0.2
0.2
0.2
......0.2
..0.2
0.2
0.2
0.2
0.2
...................E........EE....F......................EE..................................................................................Ties
preclude use of exact statistic.
..Ties preclude use of exact statistic.
.........warning: specified build_dir '_bad_path_' does not exist or
is not writable. Trying default locations
...warning: specified build_dir '..' does not exist or is not
writable. Trying default locations
..warning: specified build_dir '_bad_path_' does not exist or is not
writable. Trying default locations
...warning: specified build_dir '..' does not exist or is not
writable. Trying default locations
............................building extensions here:
/Users/Josh/.python25_compiled/m0
................................................................................................
======================================================================
ERROR: test1 (test_segment.TestSegment)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/ndimage/tests/test_segment.py",
line 12, in test1
image = get_slice(filename)
NameError: global name 'get_slice' is not defined
======================================================================
ERROR: test2 (test_segment.TestSegment)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/ndimage/tests/test_segment.py",
line 27, in test2
sourceImage, labeledMask, ROIList = segment_regions(filename)
NameError: global name 'segment_regions' is not defined
======================================================================
ERROR: test3 (test_segment.TestSegment)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/ndimage/tests/test_segment.py",
line 37, in test3
regionMask, numberRegions = grow_regions(filename)
NameError: global name 'grow_regions' is not defined
======================================================================
ERROR: Failure: ImportError (cannot import name _bspline)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/nose-0.10.1-py2.5.egg/nose/loader.py",
line 364, in loadTestsFromName
addr.filename, addr.module)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/nose-0.10.1-py2.5.egg/nose/importer.py",
line 39, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/nose-0.10.1-py2.5.egg/nose/importer.py",
line 84, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/tests/test_bspline.py",
line 9, in <module>
import scipy.stats.models.bspline as B
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/bspline.py",
line 23, in <module>
from scipy.stats.models import _bspline
ImportError: cannot import name _bspline
======================================================================
ERROR: test_factor3 (test_formula.TestFormula)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/tests/test_formula.py",
line 231, in test_factor3
m = fac.main_effect(reference=1)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/formula.py",
line 273, in main_effect
reference = names.index(reference)
ValueError: list.index(x): x not in list
======================================================================
ERROR: test_factor4 (test_formula.TestFormula)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/tests/test_formula.py",
line 239, in test_factor4
m = fac.main_effect(reference=2)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/formula.py",
line 273, in main_effect
reference = names.index(reference)
ValueError: list.index(x): x not in list
======================================================================
ERROR: test_huber (test_scale.TestScale)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/tests/test_scale.py",
line 35, in test_huber
m = scale.huber(X)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/robust/scale.py",
line 82, in __call__
for donothing in self:
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/robust/scale.py",
line 102, in next
scale = N.sum(subset * (a - mu)**2, axis=self.axis) / (self.n *
Huber.gamma - N.sum(1. - subset, axis=self.axis) * Huber.c**2)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/fromnumeric.py",
line 930, in sum
return sum(axis, dtype, out)
TypeError: only length-1 arrays can be converted to Python scalars
======================================================================
ERROR: test_huberaxes (test_scale.TestScale)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/tests/test_scale.py",
line 40, in test_huberaxes
m = scale.huber(X, axis=0)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/robust/scale.py",
line 82, in __call__
for donothing in self:
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/robust/scale.py",
line 102, in next
scale = N.sum(subset * (a - mu)**2, axis=self.axis) / (self.n *
Huber.gamma - N.sum(1. - subset, axis=self.axis) * Huber.c**2)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/fromnumeric.py",
line 930, in sum
return sum(axis, dtype, out)
TypeError: only length-1 arrays can be converted to Python scalars
======================================================================
FAIL: test_namespace (test_formula.TestFormula)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/tests/test_formula.py",
line 119, in test_namespace
self.assertEqual(xx.namespace, Y.namespace)
AssertionError: {} != {'Y': array([ 0, 2, 4, 6, 8, 10, 12, 14, 16,
18, 20, 22, 24, 26, 28, 30, 32,
34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66,
68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96,
98]), 'X': array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])}
======================================================================
SKIP: test_bytescale (test_pilutil.TestPILUtil)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: Need to import PIL for this test
======================================================================
SKIP: test_imresize (test_pilutil.TestPILUtil)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: Need to import PIL for this test
======================================================================
SKIP: Test generator for parametric tests
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/nose-0.10.1-py2.5.egg/nose/case.py",
line 203, in runTest
self.test(*self.arg)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: Need to import PIL for this test
======================================================================
SKIP: Getting factors of complex matrix
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled
======================================================================
SKIP: Getting factors of real matrix
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled
======================================================================
SKIP: Getting factors of complex matrix
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled
======================================================================
SKIP: Getting factors of real matrix
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled
======================================================================
SKIP: Prefactorize (with UMFPACK) matrix for solving with multiple rhs
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled
======================================================================
SKIP: Prefactorize matrix for solving with multiple rhs
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled
======================================================================
SKIP: Solve with UMFPACK: double precision complex
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled
======================================================================
SKIP: Solve: single precision complex
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled
======================================================================
SKIP: Solve with UMFPACK: double precision, sparse rhs
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled
======================================================================
SKIP: Solve with UMFPACK: double precision
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled
======================================================================
SKIP: Solve: single precision
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py",
line 81, in skipper
raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled
----------------------------------------------------------------------
Ran 2022 tests in 19.838s
FAILED (failures=1, errors=8)
Should I just try a clean install of SciPy at this point?
Josh
On Fri, Mar 21, 2008 at 1:38 PM, Robert Kern <robert.kern at gmail.com> wrote:
>
> On Fri, Mar 21, 2008 at 3:30 PM, Joshua Lippai <discerptor at gmail.com> wrote:
> > Hello all,
> >
> > Last night I tried installing scipy (on OS X 10.5.2) and I was
> > surprised to find that nose is now required to run scipy.test. I
> > installed it successfully through easy_install, but now it still won't
> > run the test, instead producing the following error:
> >
> > >>> scipy.test(1,10)
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in <module>
> > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/nosetester.py",
> > line 115, in test
> > argv = self._test_argv(label, verbose, extra_argv)
> > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/nosetester.py",
> > line 98, in _test_argv
> > raise TypeError, 'Selection label should be a string'
> > TypeError: Selection label should be a string
> >
> > Has anyone experienced this as well or now what's going on and how to
> > fix it so I can run scipy.test? Much thanks in advance.
>
> In [6]: scipy.test?
>
>
>
>
>
>
>
> Type: instancemethod
> Base Class: <type 'instancemethod'>
> String Form: <bound method NoseTester.test of
> <scipy.testing.nosetester.NoseTester object at 0x1b
> 2d930>>
> Namespace: Interactive
> File: /Users/rkern/svn/scipy/scipy/testing/nosetester.py
> Definition: scipy.test(self, label='fast', verbose=1,
> extra_argv=None, doctests=False)
> Docstring:
> Run tests for module using nose
>
> Parameters
> ----------
> label : {'fast', 'full', '', attribute identifer}
> Identifies test to run. This can be a string to pass to
> the nosetests executable with the'-A' option, or one of
> several special values.
> Special values are:
> 'fast' - the default - which corresponds to
> nosetests -A option of
> 'not slow'.
> 'full' - fast (as above) and slow test as in
> no -A option to nosetests - same as ''
> None or '' - run all tests
> attribute_identifier - string passed directly to
> nosetests as '-A'
> verbose : integer
> verbosity value for test outputs, 1-10
> extra_argv : list
> List with any extra args to pass to nosetests
> doctests : boolean
> If True, run doctests in module, default False
>
> --
> 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
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>
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