[Bug 299375] [NEW] scipy test fails

Tue Nov 18 08:55:30 UTC 2008

Public bug reported:

I am running Ubuntu 8.10, updated from 8.04 -- installed python and
scipy with aptitude from the repositories.

Best,
Sebastian.

sbusch at tof8:~$ uname -a
Linux tof8 2.6.24-21-generic #1 SMP Tue Oct 21 23:09:30 UTC 2008 x86_64 GNU/Linux
sbusch at tof8:~$ python
Python 2.5.2 (r252:60911, Oct  5 2008, 19:29:17) 
[GCC 4.3.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.__version__
'1.1.1'
>>> numpy.test()
Numpy is installed in /usr/lib/python2.5/site-packages/numpy
Numpy version 1.1.1
Python version 2.5.2 (r252:60911, Oct  5 2008, 19:29:17) [GCC 4.3.2]
  Found 63/63 tests for numpy.core.tests.test_unicode
  Found 72/72 tests for numpy.core.tests.test_numeric
  Found 12/12 tests for numpy.core.tests.test_records
  Found 36/36 tests for numpy.core.tests.test_numerictypes
  Found 2/2 tests for numpy.core.tests.test_ufunc
  Found 145/145 tests for numpy.core.tests.test_regression
  Found 3/3 tests for numpy.core.tests.test_errstate
  Found 3/3 tests for numpy.core.tests.test_memmap
  Found 16/16 tests for numpy.core.tests.test_umath
  Found 7/7 tests for numpy.core.tests.test_scalarmath
  Found 18/18 tests for numpy.core.tests.test_defmatrix
  Found 290/290 tests for numpy.core.tests.test_multiarray
  Found 5/5 tests for numpy.distutils.tests.test_misc_util
  Found 4/4 tests for numpy.distutils.tests.test_fcompiler_gnu
  Found 2/2 tests for numpy.fft.tests.test_fftpack
  Found 3/3 tests for numpy.fft.tests.test_helper
  Found 15/15 tests for numpy.lib.tests.test_twodim_base
  Found 10/10 tests for numpy.lib.tests.test_arraysetops
  Found 1/1 tests for numpy.lib.tests.test_ufunclike
  Found 5/5 tests for numpy.lib.tests.test_getlimits
  Found 25/25 tests for numpy.lib.tests.test__datasource
  Found 1/1 tests for numpy.lib.tests.test_regression
  Found 1/1 tests for numpy.lib.tests.test_machar
  Found 55/55 tests for numpy.lib.tests.test_function_base
  Found 15/15 tests for numpy.lib.tests.test_io
  Found 49/49 tests for numpy.lib.tests.test_shape_base
  Found 1/1 tests for numpy.lib.tests.test_financial
  Found 43/43 tests for numpy.lib.tests.test_type_check
  Found 6/6 tests for numpy.lib.tests.test_index_tricks
  Found 4/4 tests for numpy.lib.tests.test_polynomial
  Found 3/3 tests for numpy.linalg.tests.test_regression
  Found 89/89 tests for numpy.linalg.tests.test_linalg
  Found 4/4 tests for numpy.ma.tests.test_subclassing
  Found 36/36 tests for numpy.ma.tests.test_old_ma
  Found 19/19 tests for numpy.ma.tests.test_mrecords
  Found 96/96 tests for numpy.ma.tests.test_core
  Found 15/15 tests for numpy.ma.tests.test_extras
  Found 1/1 tests for numpy.oldnumeric.tests.test_oldnumeric
  Found 7/7 tests for numpy.tests.test_random
  Found 16/16 tests for numpy.testing.tests.test_utils
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 1286 tests in 2.653s

OK
<unittest._TextTestResult run=1286 errors=0 failures=0>
>>> import scipy
>>> scipy.__version__
'0.6.0'
>>> scipy.test()
  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 10/10 tests for scipy.integrate.tests.test_quadpack
  Found 1/1 tests for scipy.integrate.tests.test_integrate
  Found 6/6 tests for scipy.tests.test_interpolate
  Found 6/6 tests for scipy.tests.test_fitpack
  Found 5/5 tests for scipy.io.tests.test_npfile
  Found 28/28 tests for scipy.io.tests.test_mio
  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 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
Failed importing /usr/lib/python2.5/site-packages/scipy/linalg/tests/test_iterative.py: cannot import name iterative
Failed importing /usr/lib/python2.5/site-packages/scipy/linalg/tests/test_fblas.py: cannot import name fblas
Failed importing /usr/lib/python2.5/site-packages/scipy/linalg/tests/test_matfuncs.py: cannot import name signm
Failed importing /usr/lib/python2.5/site-packages/scipy/linalg/tests/test_lapack.py: cannot import name flapack
Failed importing /usr/lib/python2.5/site-packages/scipy/linalg/tests/test_blas.py: cannot import name fblas
Failed importing /usr/lib/python2.5/site-packages/scipy/linalg/tests/test_basic.py: cannot import name toeplitz
Failed importing /usr/lib/python2.5/site-packages/scipy/linalg/tests/test_decomp.py: cannot import name lu
  Found 9/9 tests for scipy.linsolve.umfpack.tests.test_umfpack
  Found 2/2 tests for scipy.maxentropy.tests.test_maxentropy
  Found 3/3 tests for scipy.misc.tests.test_pilutil
  Found 399/399 tests for scipy.tests.test_ndimage
  Found 5/5 tests for scipy.odr.tests.test_odr
  Found 10/10 tests for scipy.optimize.tests.test_nonlin
  Found 4/4 tests for scipy.optimize.tests.test_zeros
  Found 1/1 tests for scipy.optimize.tests.test_cobyla
  Found 8/8 tests for scipy.optimize.tests.test_optimize
  Found 4/4 tests for scipy.signal.tests.test_wavelets
  Found 5/5 tests for scipy.signal.tests.test_signaltools
  Found 152/152 tests for scipy.sparse.tests.test_sparse
  Found 3/3 tests for scipy.special.tests.test_spfun_stats
  Found 342/342 tests for scipy.special.tests.test_basic
  Found 73/73 tests for scipy.stats.tests.test_distributions
  Found 107/107 tests for scipy.stats.tests.test_stats
  Found 10/10 tests for scipy.stats.tests.test_morestats
  Found 1/1 tests for scipy.weave.tests.test_ast_tools
  Found 0/0 tests for scipy.weave.tests.test_scxx_object
  Found 0/0 tests for scipy.weave.tests.test_inline_tools
  Found 0/0 tests for scipy.weave.tests.test_scxx_sequence
  Found 0/0 tests for scipy.weave.tests.test_scxx_dict
  Found 0/0 tests for scipy.weave.tests.test_wx_spec
building extensions here: /home/toftof/sbusch/.python25_compiled/m4
  Found 1/1 tests for scipy.weave.tests.test_ext_tools
  Found 2/2 tests for scipy.weave.tests.test_blitz_tools
  Found 26/26 tests for scipy.weave.tests.test_catalog
  Found 16/16 tests for scipy.weave.tests.test_slice_handler
  Found 0/0 tests for scipy.weave.tests.test_c_spec
  Found 3/3 tests for scipy.weave.tests.test_standard_array_spec
  Found 9/9 tests for scipy.weave.tests.test_build_tools
  Found 74/74 tests for scipy.weave.tests.test_size_check
.../usr/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.
.............................................................Residual: 1.05006987327e-07
......./usr/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.
.......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.................Use minimum degree ordering on A'+A.
..Use minimum degree ordering on A'+A.
F..Use minimum degree ordering on A'+A.
F............................................................................................................/usr/lib/python2.5/site-packages/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 '
........................................................................................................................................................................................................................................................................................................F..F.........................................................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.
......................................................................................................................................................................................................................F................................................................................................................................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.
.......................................................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 "/usr/lib/python2.5/site-packages/scipy/lib/lapack/tests/esv_tests.py", line 41, in check_syevr
    assert_array_almost_equal(w,exact_w)
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/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,  0.48769474,  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 "/usr/lib/python2.5/site-packages/scipy/lib/lapack/tests/esv_tests.py", line 66, in check_syevr_irange
    assert_array_almost_equal(w,exact_w[rslice])
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/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,  0.48769474,  9.18222618], dtype=float32)
 y: array([-0.66992434,  0.48769389,  9.18223045])

======================================================================
FAIL: Solve: single precision complex
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.5/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py", line 32, in check_solve_complex_without_umfpack
    assert_array_almost_equal(a*x, b)
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 240, in assert_array_compare
    assert cond, msg
AssertionError: 
Arrays are not almost equal

(mismatch 20.0%)
 x: array([ 1.00000000+0.j,  1.99999809+0.j,  3.00000000+0.j,  4.00000048+0.j,
        5.00000000+0.j], dtype=complex64)
 y: array([1, 2, 3, 4, 5])

======================================================================
FAIL: Solve: single precision
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.5/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py", line 43, in check_solve_without_umfpack
    assert_array_almost_equal(a*x, b)
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 240, in assert_array_compare
    assert cond, msg
AssertionError: 
Arrays are not almost equal

(mismatch 20.0%)
 x: array([ 1.        ,  1.99999809,  3.        ,  4.00000048,  5.        ], dtype=float32)
 y: array([1, 2, 3, 4, 5])

======================================================================
FAIL: test_explicit (scipy.odr.tests.test_odr.test_odr)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.5/site-packages/scipy/odr/tests/test_odr.py", line 50, in test_explicit
    -8.7849712165253724e-02]),
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 240, in assert_array_compare
    assert cond, msg
AssertionError: 
Arrays are not almost equal

(mismatch 100.0%)
 x: array([  1.26462971e+03,  -5.42545890e+01,  -8.64250389e-02])
 y: array([  1.26465481e+03,  -5.40184100e+01,  -8.78497122e-02])

======================================================================
FAIL: test_multi (scipy.odr.tests.test_odr.test_odr)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.5/site-packages/scipy/odr/tests/test_odr.py", line 191, in test_multi
    0.5101147161764654,  0.5173902330489161]),
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 240, in assert_array_compare
    assert cond, msg
AssertionError: 
Arrays are not almost equal

(mismatch 100.0%)
 x: array([ 4.31272063,  2.44289312,  7.76215871,  0.55995622,  0.46423343])
 y: array([ 4.37998803,  2.43330576,  8.00288459,  0.51011472,  0.51739023])

======================================================================
FAIL: check_pbdv (scipy.special.tests.test_basic.test_cephes)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.5/site-packages/scipy/special/tests/test_basic.py", line 368, in check_pbdv
    assert_equal(cephes.pbdv(1,0),(0.0,0.0))
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 139, in assert_equal
    assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose)
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 145, in assert_equal
    assert desired == actual, msg
AssertionError: 
Items are not equal:
item=1

 ACTUAL: 1.0
 DESIRED: 0.0

----------------------------------------------------------------------
Ran 1586 tests in 9.031s

FAILED (failures=7)
<unittest._TextTestResult run=1586 errors=0 failures=7>
>>>

** Affects: python-scipy (Ubuntu)
     Importance: Undecided
         Status: New

-- 
scipy test fails
https://bugs.launchpad.net/bugs/299375
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