[SciPy-user] scipy.test fails: clapack module is empty

Bryan Keith bryan@ideotrope....
Tue Sep 9 11:48:14 CDT 2008


Hello,

I'm trying to install scipy (0.6.0) on Ubuntu 8.04 64 bit with Python
2.5.2 and numpy 1.0.4

Installation (via apt-get) seems to go fine, but the test suite fails. 
I'm not sure how concerned I should be about this failure.  I've searched
for some of the errors that I'm getting but couldn't find anything to
either resolve the tests and make me decide to ignore them.  I'm pasting
the test results below.  Any help is appreciated.  Thank you.

Bryan

>>> import scipy
>>> scipy.test(level=1)
  Found 9/9 tests for scipy.cluster.vq
  Found 18/18 tests for scipy.fftpack.basic
  Found 4/4 tests for scipy.fftpack.helper
  Found 20/20 tests for scipy.fftpack.pseudo_diffs
  Found 1/1 tests for scipy.integrate
  Found 10/10 tests for scipy.integrate.quadpack
  Found 3/3 tests for scipy.integrate.quadrature
  Found 6/6 tests for scipy.interpolate
  Found 6/6 tests for scipy.interpolate.fitpack
  Found 4/4 tests for scipy.io.array_import
  Found 28/28 tests for scipy.io.mio
  Found 13/13 tests for scipy.io.mmio
  Found 5/5 tests for scipy.io.npfile
  Found 4/4 tests for scipy.io.recaster
  Found 16/16 tests for scipy.lib.blas
  Found 128/128 tests for scipy.lib.blas.fblas

****************************************************************
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
  Found 41/41 tests for scipy.linalg.basic
<module 'scipy.linalg.fblas' from
'/usr/lib/python2.5/site-packages/scipy/linalg/fblas.so'>
  Found 16/16 tests for scipy.linalg.blas
  Found 72/72 tests for scipy.linalg.decomp
  Found 128/128 tests for scipy.linalg.fblas
  Found 6/6 tests for scipy.linalg.iterative
  Found 4/4 tests for scipy.linalg.lapack
  Found 7/7 tests for scipy.linalg.matfuncs
  Found 9/9 tests for scipy.linsolve.umfpack
  Found 2/2 tests for scipy.maxentropy
  Found 3/3 tests for scipy.misc.pilutil
  Found 399/399 tests for scipy.ndimage
  Found 5/5 tests for scipy.odr
  Found 8/8 tests for scipy.optimize
  Found 1/1 tests for scipy.optimize.cobyla
  Found 10/10 tests for scipy.optimize.nonlin
  Found 4/4 tests for scipy.optimize.zeros
  Found 5/5 tests for scipy.signal.signaltools
  Found 4/4 tests for scipy.signal.wavelets
  Found 152/152 tests for scipy.sparse
  Found 342/342 tests for scipy.special.basic
  Found 3/3 tests for scipy.special.spfun_stats
  Found 107/107 tests for scipy.stats
  Found 73/73 tests for scipy.stats.distributions
  Found 10/10 tests for scipy.stats.morestats
  Found 0/0 tests for __main__
.../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.......................................................
****************************************************************
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 = 1.11929781998e-08
...Result may be inaccurate, approximate err = 7.73070496507e-12
......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.
....................................................................................................................................................................................................................................................................................................................................................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.
......
======================================================================
FAIL: check_syevr (scipy.lib.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
232, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
217, 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.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
232, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
217, 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
232, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
217, 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
232, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
217, 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.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
232, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
217, 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.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
232, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
217, 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])

----------------------------------------------------------------------
Ran 1728 tests in 7.579s

FAILED (failures=6)
<unittest._TextTestResult run=1728 errors=0 failures=6>
>>>




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