[SciPy-user] Some failing tests

Nils Wagner nwagner@iam.uni-stuttgart...
Mon Oct 6 11:40:05 CDT 2008


On Mon, 6 Oct 2008 11:26:25 -0500
  chris <cdcasey@gmail.com> wrote:
> Sorry. That should have read RedHat 4 32-bit (not 3 & 
>4). Also, using
> numpy 1.1.1.
> 
> On Mon, Oct 6, 2008 at 11:19 AM, chris 
><cdcasey@gmail.com> wrote:
>> when i run scipy.test() on RedHat 32-bit 3 & 4, I get 
>>the following
>> feedback. Are these things I need to worry about? It's 
>>running scipy
>> 0.6.0. Not sure if these are fixed in the next version, 
>>or if there's
>> a way I can fix them now....
>>
>>
>>>>> import scipy
>>>>> scipy.test()
>> Failed importing scipy.linsolve.umfpack: 'module' object 
>>has no
>> attribute 'umfpack'
>>  Found 9/9 tests for scipy.cluster.tests.test_vq
>>  Found 20/20 tests for 
>>scipy.fftpack.tests.test_pseudo_diffs
>>  Found 4/4 tests for scipy.fftpack.tests.test_helper
>>  Found 18/18 tests for scipy.fftpack.tests.test_basic
>>  Found 3/3 tests for 
>>scipy.integrate.tests.test_quadrature
>>  Found 1/1 tests for 
>>scipy.integrate.tests.test_integrate
>>  Found 10/10 tests for 
>>scipy.integrate.tests.test_quadpack
>>  Found 6/6 tests for scipy.tests.test_interpolate
>>  Found 6/6 tests for scipy.tests.test_fitpack
>>  Found 13/13 tests for scipy.io.tests.test_mmio
>>  Found 4/4 tests for scipy.io.tests.test_recaster
>>  Found 4/4 tests for scipy.io.tests.test_array_import
>>  Found 5/5 tests for scipy.io.tests.test_npfile
>>  Found 28/28 tests for scipy.io.tests.test_mio
>>  Found 128/128 tests for scipy.lib.blas.tests.test_fblas
>>  Found 16/16 tests for scipy.lib.blas.tests.test_blas
>>
>> ****************************************************************
>> 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.
>> ****************************************************************
>>
>>  Found 42/42 tests for 
>>scipy.lib.lapack.tests.test_lapack
>>  Found 6/6 tests for scipy.linalg.tests.test_iterative
>>  Found 41/41 tests for scipy.linalg.tests.test_basic
>>  Found 128/128 tests for scipy.linalg.tests.test_fblas
>>  Found 72/72 tests for scipy.linalg.tests.test_decomp
>>  Found 4/4 tests for scipy.linalg.tests.test_lapack
>> <module 'scipy.linalg.fblas' from
>> '/home/ccasey/epd/lib/python2.5/site-packages/scipy-0.6.0.0006_s-py2.5-linux-i686.egg/scipy/linalg/fblas.so'>
>>  Found 16/16 tests for scipy.linalg.tests.test_blas
>>  Found 7/7 tests for scipy.linalg.tests.test_matfuncs
>> Failed importing
>> /home/ccasey/epd/lib/python2.5/site-packages/scipy-0.6.0.0006_s-py2.5-linux-i686.egg/scipy/linsolve/umfpack/tests/test_umfpack.py:
>> 'module' object has no attribute 'umfpack'
>>  Found 2/2 tests for 
>>scipy.maxentropy.tests.test_maxentropy
>>  Found 3/3 tests for scipy.tests.test_pilutil
>>  Found 395/395 tests for 
>>scipy.ndimage.tests.test_ndimage
>>  Found 5/5 tests for scipy.odr.tests.test_odr
>>  Found 8/8 tests for scipy.optimize.tests.test_optimize
>>  Found 1/1 tests for scipy.optimize.tests.test_cobyla
>>  Found 10/10 tests for scipy.optimize.tests.test_nonlin
>>  Found 4/4 tests for scipy.optimize.tests.test_zeros
>>  Found 5/5 tests for scipy.signal.tests.test_signaltools
>>  Found 4/4 tests for scipy.signal.tests.test_wavelets
>>  Found 152/152 tests for scipy.sparse.tests.test_sparse
>>  Found 342/342 tests for scipy.special.tests.test_basic
>>  Found 3/3 tests for 
>>scipy.special.tests.test_spfun_stats
>>  Found 10/10 tests for scipy.stats.tests.test_morestats
>>  Found 107/107 tests for scipy.stats.tests.test_stats
>>  Found 73/73 tests for 
>>scipy.stats.tests.test_distributions
>> building extensions here: 
>>/home/ccasey/.python25_compiled/m10
>>  Found 1/1 tests for scipy.weave.tests.test_ext_tools
>>  Found 0/0 tests for scipy.weave.tests.test_c_spec
>>  Found 74/74 tests for scipy.weave.tests.test_size_check
>>  Found 2/2 tests for scipy.weave.tests.test_blitz_tools
>>  Found 0/0 tests for scipy.weave.tests.test_scxx_object
>>  Found 0/0 tests for scipy.weave.tests.test_scxx_dict
>>  Found 0/0 tests for 
>>scipy.weave.tests.test_scxx_sequence
>>  Found 26/26 tests for scipy.weave.tests.test_catalog
>>  Found 1/1 tests for scipy.weave.tests.test_ast_tools
>>  Found 0/0 tests for scipy.weave.tests.test_inline_tools
>>  Found 3/3 tests for 
>>scipy.weave.tests.test_standard_array_spec
>> Failed importing
>> /home/ccasey/epd/lib/python2.5/site-packages/scipy-0.6.0.0006_s-py2.5-linux-i686.egg/scipy/weave/tests/test_wx_spec.py:
>> Could not locate wxPython base directory.
>>  Found 16/16 tests for 
>>scipy.weave.tests.test_slice_handler
>>  Found 9/9 tests for scipy.weave.tests.test_build_tools
>> .../home/ccasey/epd/lib/python2.5/site-packages/scipy-0.6.0.0006_s-py2.5-linux-i686.egg/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.
>> ...................................................Residual: 
>>1.05006950608e-07
>> ................./home/ccasey/epd/lib/python2.5/site-packages/scipy-0.6.0.0006_s-py2.5-linux-i686.egg/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.
>> ........................................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
>> ............................................FF................................................................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.
>> ****************************************************************
>>
>> ..
>> ****************************************************************
>> 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.
>> ****************************************************************
>>
>> .................Result may be inaccurate, approximate 
>>err = 5.71185593749e-09
>> ................................................................................................................../home/ccasey/epd/lib/python2.5/site-packages/scipy-0.6.0.0006_s-py2.5-linux-i686.egg/scipy/ndimage/interpolation.py:41:
>> UserWarning: Mode "reflect" may yield incorrect results 
>>on boundaries.
>> Please use "mirror" instead.
>>  warnings.warn('Mode "reflect" may yield incorrect 
>>results on '
>> .................................................................................................................................................................................................................................................................................................................................................................Use
>> minimum degree ordering on A'+A.
>> .....................................Use minimum degree 
>>ordering on A'+A.
>> .....................................Use minimum degree 
>>ordering on A'+A.
>> ................................Use minimum degree 
>>ordering on A'+A.
>> ....................................................................................................................................................................................................................................................................................................................................................0.2
>> 0.2
>> 0.2
>> ......0.2
>> ..0.2
>> 0.2
>> 0.2
>> 0.2
>> 0.2
>> .....................Ties preclude use of exact 
>>statistic.
>> ..Ties preclude use of exact statistic.
>> ......................./home/ccasey/epd/lib/python2.5/site-packages/numpy-1.1.1.0001-py2.5-linux-i686.egg/numpy/lib/function_base.py:166:
>> FutureWarning:
>>        The semantics of histogram will be modified in
>>        release 1.2 to improve outlier handling. The new 
>>behavior can be
>>        obtained using new=True. Note that the new 
>>version accepts/returns
>>        the bin edges instead of the left bin edges.
>>        Please read the docstring for more information.
>>  Please read the docstring for more information.""", 
>>FutureWarning)
>> /home/ccasey/epd/lib/python2.5/site-packages/numpy-1.1.1.0001-py2.5-linux-i686.egg/numpy/lib/function_base.py:181:
>> FutureWarning:
>>                Outliers handling will change in version 
>>1.2.
>>                Please read the docstring for details.
>>  Please read the docstring for details.""", 
>>FutureWarning)
>> ..............................................................................................................................................................................................................................................................................................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
>> .
>> ======================================================================
>> FAIL: check_syevr 
>>(scipy.lib.lapack.tests.test_lapack.test_flapack_float)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>  File 
>>"/home/ccasey/epd/lib/python2.5/site-packages/scipy-0.6.0.0006_s-py2.5-linux-i686.egg/scipy/lib/lapack/tests/esv_tests.py",
>> line 41, in check_syevr
>>    assert_array_almost_equal(w,exact_w)
>>  File 
>>"/home/ccasey/epd/lib/python2.5/site-packages/numpy-1.1.1.0001-py2.5-linux-i686.egg/numpy/testing/utils.py",
>> line 255, in assert_array_almost_equal
>>    header='Arrays are not almost equal')
>>  File 
>>"/home/ccasey/epd/lib/python2.5/site-packages/numpy-1.1.1.0001-py2.5-linux-i686.egg/numpy/testing/utils.py",
>> line 240, in assert_array_compare
>>    assert cond, msg
>> AssertionError:
>> Arrays are not almost equal
>>
>> (mismatch 33.3333333333%)
>>  x: array([-0.66992444,  0.48769444,  9.18222618], 
>>dtype=float32)
>>  y: array([-0.66992434,  0.48769389,  9.18223045])
>>
>> ======================================================================
>> FAIL: check_syevr_irange
>> (scipy.lib.lapack.tests.test_lapack.test_flapack_float)----------------------------------------------------------------------
>> Traceback (most recent call last):
>>  File 
>>"/home/ccasey/epd/lib/python2.5/site-packages/scipy-0.6.0.0006_s-py2.5-linux-i686.egg/scipy/lib/lapack/tests/esv_tests.py",
>> line 66, in check_syevr_irange
>>    assert_array_almost_equal(w,exact_w[rslice])
>>  File 
>>"/home/ccasey/epd/lib/python2.5/site-packages/numpy-1.1.1.0001-py2.5-linux-i686.egg/numpy/testing/utils.py",
>> line 255, in assert_array_almost_equal
>>    header='Arrays are not almost equal')
>>  File 
>>"/home/ccasey/epd/lib/python2.5/site-packages/numpy-1.1.1.0001-py2.5-linux-i686.egg/numpy/testing/utils.py",
>> line 240, in assert_array_compare
>>    assert cond, msg
>> AssertionError:
>> Arrays are not almost equal
>>
>> (mismatch 33.3333333333%)
>>  x: array([-0.66992444,  0.48769444,  9.18222618], 
>>dtype=float32)
>>  y: array([-0.66992434,  0.48769389,  9.18223045])
>>
>> ----------------------------------------------------------------------
>> Ran 1847 tests in 6.389s
>>
>> FAILED (failures=2)
>> <unittest._TextTestResult run=1847 errors=0 failures=2>
>>
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This is a known issue
See
http://scipy.org/scipy/scipy/ticket/375

  
Nils


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