[SciPy-user] Test failure on OS X Leopard

Jonathan Hunt jjh@42quarks....
Mon Jun 23 00:59:53 CDT 2008


Hi,

I installed NumPy (1.1) and SciPy (0.6) both from source on OS X
(Leopard 10.5.3) . I removed existing numpy/scipy libraries. Both
install with no errors. And numpy.test() passes all tests. However,
running:

>>> import scipy
>>> scipy.test();
fails with:
....................................................................................................................warning:
specified build_dir '_bad_path_' 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
............................................................................................................................
======================================================================
FAIL: check_dot (scipy.lib.blas.tests.test_blas.test_fblas1_simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Python/2.5/site-packages/scipy/lib/blas/tests/test_blas.py",
line 76, in check_dot
    assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j)
  File "/Library/Python/2.5/site-packages/numpy/testing/utils.py",
line 158, in assert_almost_equal
    assert round(abs(desired - actual),decimal) == 0, msg
AssertionError:
Items are not equal:
 ACTUAL: 2.1796638438433325e-36j
 DESIRED: (-9+2j)

----------------------------------------------------------------------
Ran 1574 tests in 5.679s

FAILED (failures=1)
<unittest._TextTestResult run=1574 errors=0 failures=1>


Is this bad? A problem? It seems to be related to LAPACK/BLAS but on
install SciPy said it detected LAPACK/BLAST.

Any help appreciated.

Thanks,
Jonny





Full test output is appended below:
Failed importing scipy.linsolve.umfpack: 'module' object has no
attribute 'umfpack'
  Found 9/9 tests for scipy.cluster.tests.test_vq
  Found 18/18 tests for scipy.fftpack.tests.test_basic
  Found 4/4 tests for scipy.fftpack.tests.test_helper
  Found 20/20 tests for scipy.fftpack.tests.test_pseudo_diffs
  Found 1/1 tests for scipy.integrate.tests.test_integrate
  Found 10/10 tests for scipy.integrate.tests.test_quadpack
  Found 3/3 tests for scipy.integrate.tests.test_quadrature
  Found 6/6 tests for scipy.tests.test_fitpack
  Found 6/6 tests for scipy.tests.test_interpolate
  Found 4/4 tests for scipy.io.tests.test_array_import
  Found 28/28 tests for scipy.io.tests.test_mio
  Found 13/13 tests for scipy.io.tests.test_mmio
  Found 5/5 tests for scipy.io.tests.test_npfile
  Found 4/4 tests for scipy.io.tests.test_recaster
  Found 16/16 tests for scipy.lib.blas.tests.test_blas
  Found 128/128 tests for scipy.lib.blas.tests.test_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.tests.test_lapack
  Found 41/41 tests for scipy.linalg.tests.test_basic
<module 'scipy.linalg.fblas' from
'/Library/Python/2.5/site-packages/scipy/linalg/fblas.so'>
  Found 16/16 tests for scipy.linalg.tests.test_blas
  Found 72/72 tests for scipy.linalg.tests.test_decomp
  Found 128/128 tests for scipy.linalg.tests.test_fblas
  Found 6/6 tests for scipy.linalg.tests.test_iterative
  Found 4/4 tests for scipy.linalg.tests.test_lapack
  Found 7/7 tests for scipy.linalg.tests.test_matfuncs
Failed importing
/Library/Python/2.5/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py:
'module' object has no attribute 'umfpack'
  Found 2/2 tests for scipy.maxentropy.tests.test_maxentropy
Failed importing
/Library/Python/2.5/site-packages/scipy/misc/tests/test_pilutil.py: No
module named PIL.Image
  Found 399/399 tests for scipy.ndimage.tests.test_ndimage
  Found 5/5 tests for scipy.odr.tests.test_odr
  Found 1/1 tests for scipy.optimize.tests.test_cobyla
  Found 10/10 tests for scipy.optimize.tests.test_nonlin
  Found 8/8 tests for scipy.optimize.tests.test_optimize
  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 73/73 tests for scipy.stats.tests.test_distributions
  Found 10/10 tests for scipy.stats.tests.test_morestats
  Found 107/107 tests for scipy.stats.tests.test_stats
  Found 1/1 tests for scipy.weave.tests.test_ast_tools
  Found 2/2 tests for scipy.weave.tests.test_blitz_tools
  Found 9/9 tests for scipy.weave.tests.test_build_tools
  Found 0/0 tests for scipy.weave.tests.test_c_spec
  Found 26/26 tests for scipy.weave.tests.test_catalog
building extensions here: /Users/uqjhunt2/.python25_compiled/m5
  Found 1/1 tests for scipy.weave.tests.test_ext_tools
  Found 0/0 tests for scipy.weave.tests.test_inline_tools
  Found 0/0 tests for scipy.weave.tests.test_scxx_dict
  Found 0/0 tests for scipy.weave.tests.test_scxx_object
  Found 0/0 tests for scipy.weave.tests.test_scxx_sequence
  Found 74/74 tests for scipy.weave.tests.test_size_check
  Found 16/16 tests for scipy.weave.tests.test_slice_handler
  Found 3/3 tests for scipy.weave.tests.test_standard_array_spec
  Found 0/0 tests for scipy.weave.tests.test_wx_spec
.../Library/Python/2.5/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: 1.05006987366e-07
............../Library/Python/2.5/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.
..............................................................F..........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: 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
............................................................................................................/Library/Python/2.5/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 '
.....................................................................................................................................................................................................................................................................................................................................................................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.
......................./Library/Python/2.5/site-packages/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)
/Library/Python/2.5/site-packages/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 '_bad_path_' does not exist or is
not writable. Trying default locations
............................................................................................................................
======================================================================
FAIL: check_dot (scipy.lib.blas.tests.test_blas.test_fblas1_simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Python/2.5/site-packages/scipy/lib/blas/tests/test_blas.py",
line 76, in check_dot
    assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j)
  File "/Library/Python/2.5/site-packages/numpy/testing/utils.py",
line 158, in assert_almost_equal
    assert round(abs(desired - actual),decimal) == 0, msg
AssertionError:
Items are not equal:
 ACTUAL: 8.5864323499206074e-37j
 DESIRED: (-9+2j)

----------------------------------------------------------------------
Ran 1848 tests in 6.136s

FAILED (failures=1)
<unittest._TextTestResult run=1848 errors=0 failures=1>
>>>


-- 
Jonathan J Hunt <jjh@42quarks.com>
Homepage: http://www.42quarks.net.nz/wiki/JJH
(Further contact details there)
"Physics isn't the most important thing. Love is." Richard Feynman


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