[SciPy-User] many test failures on windows 64

Robin robince@gmail....
Mon Jul 5 05:40:58 CDT 2010


Hi,

I am using Python.org amd64 python build on windows 7 64 bit.

I am using numpy and scipy builds from here:
http://www.lfd.uci.edu/~gohlke/pythonlibs/

I get many errors in scipy test (none for numpy). Particularly in
scipy.sparse.linalg which I need to use (and in my code it appears
spsolve is giving incorrect results).

Is there a better 64 bit windows build to use?

>>> scipy.test()
Running unit tests for scipy
NumPy version 1.4.1
NumPy is installed in C:\Python26\lib\site-packages\numpy
SciPy version 0.8.0b1
SciPy is installed in C:\Python26\lib\site-packages\scipy
Python version 2.6.5 (r265:79096, Mar 19 2010, 18:02:59) [MSC v.1500
64 bit (AMD64)]
nose version 0.11.3
........................................................................................................................
............................E....................................F......................................................
..............................C:\Python26\lib\site-packages\scipy\interpolate\fitpack2.py:639:
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)
.....C:\Python26\lib\site-packages\scipy\interpolate\fitpack2.py:580:
UserWarning:
The required storage space exceeds the available storage space: nxest
or nyest too small, or s too small.
The weighted least-squares spline corresponds to the current set of
knots.
  warnings.warn(message)
...........................................K..K.........................................................................
........................................................................................................................
........................................................................................................................
EC:\Python26\lib\site-packages\numpy\lib\utils.py:140:
DeprecationWarning: `write_array` is deprecated!

This function is replaced by numpy.savetxt which allows the same functionality
through a different syntax.

  warnings.warn(depdoc, DeprecationWarning)
C:\Python26\lib\site-packages\numpy\lib\utils.py:140:
DeprecationWarning: `read_array` is deprecated!

The functionality of read_array is in numpy.loadtxt which allows the same
functionality using different syntax.

  warnings.warn(depdoc, DeprecationWarning)
...........................................Exception AttributeError:
"'netcdf_file' object has no attribute 'mode'" in <
bound method netcdf_file.close of <scipy.io.netcdf.netcdf_file object
at 0x000000000C64D6D8>> ignored
............C:\Python26\lib\site-packages\numpy\lib\utils.py:140:
DeprecationWarning: `npfile` is deprecated!

You can achieve the same effect as using npfile using numpy.save and
numpy.load.

You can use memory-mapped arrays and data-types to map out a
file format for direct manipulation in NumPy.

  warnings.warn(depdoc, DeprecationWarning)
.........C:\Python26\lib\site-packages\scipy\io\wavfile.py:30:
WavFileWarning: Unfamiliar format bytes
  warnings.warn("Unfamiliar format bytes", WavFileWarning)
C:\Python26\lib\site-packages\scipy\io\wavfile.py:120: WavFileWarning:
chunk not understood
  warnings.warn("chunk not understood", WavFileWarning)
........................................................................................................................
.......................................................................................................SSSSSS......SSSSS
S......SSSS...............................................................S.............................................
........................................................................................................................
..............................................E.........................................................................
........................................................................................................................
....SSS.........S.......................................................................................................
.............................................................F..........................................................
........................................................................................................................
.....................................................FFF.....................................................C:\Python26
\lib\site-packages\scipy\signal\filter_design.py:247: BadCoefficients:
Badly conditioned filter coefficients (numerator)
: the results may be meaningless
  "results may be meaningless", BadCoefficients)
........................................................................................................................
................................................................................................E.......................
..........................SSSSSSSSSSS.FE.EE.EE......K.........E.E...................................E...................
....................................................................K..................E................................
............K..................E.................................................E......................................
..............................................KK........................E...............................................
........................................................................................................................
..................................................................................................................F.....
...............................................................................K.K......................................
........................................................................................................................
........................................................................................................................
..........................F...F..............................................................K........K.........SSSSS...
........................................................................................................................
........................................................................................................................
........................................................................................................................
........................................................................................................................
.............................S..........................................................................................
...........................................................................................C:\Python26\lib\site-packages
\scipy\stats\morestats.py:702: UserWarning: Ties preclude use of exact
statistic.
  warnings.warn("Ties preclude use of exact statistic.")
........................................................................................................................
........................................................................................................................
....................................................error removing
c:\users\robince\appdata\local\temp\tmpr3s_aecat_test
: c:\users\robince\appdata\local\temp\tmpr3s_aecat_test: The directory
is not empty
..................................................................................................
======================================================================
ERROR: Testing that kmeans2 init methods work.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\cluster\tests\test_vq.py",
line 166, in test_kmeans2_init
    kmeans2(data, 3, minit = 'points')
  File "C:\Python26\lib\site-packages\scipy\cluster\vq.py", line 671, in kmeans2
    clusters = init(data, k)
  File "C:\Python26\lib\site-packages\scipy\cluster\vq.py", line 523,
in _kpoints
    p = np.random.permutation(n)
  File "mtrand.pyx", line 4231, in mtrand.RandomState.permutation
(build\scons\numpy\random\mtrand\mtrand.c:18669)
  File "mtrand.pyx", line 4174, in mtrand.RandomState.shuffle
(build\scons\numpy\random\mtrand\mtrand.c:18261)
TypeError: len() of unsized object

======================================================================
ERROR: test_basic (test_array_import.TestNumpyio)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\io\tests\test_array_import.py",
line 29, in test_basic
    b = numpyio.fread(fid,1000000,N.Int16,N.Int)
MemoryError

======================================================================
ERROR: test_decomp.test_lapack_misaligned(<function solve at
0x0000000006366438>, (array([[  1.734e-255,   8.189e-217,
 4.025e-178,   1.903e-139,   9.344e-101,
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py",
line 186, in runTest
    self.test(*self.arg)
  File "C:\Python26\lib\site-packages\scipy\linalg\tests\test_decomp.py",
line 1074, in check_lapack_misaligned
    func(*a,**kwargs)
  File "C:\Python26\lib\site-packages\scipy\linalg\basic.py", line 49, in solve
    a1, b1 = map(asarray_chkfinite,(a,b))
  File "C:\Python26\lib\site-packages\numpy\lib\function_base.py",
line 586, in asarray_chkfinite
    raise ValueError, "array must not contain infs or NaNs"
ValueError: array must not contain infs or NaNs

======================================================================
ERROR: Regression test for #880: empty array for zi crashes.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\signal\tests\test_signaltools.py",
line 422, in test_empty_zi
    y, zf = lfilter(b, a, x, zi=zi)
  File "C:\Python26\lib\site-packages\scipy\signal\signaltools.py",
line 610, in lfilter
    return sigtools._linear_filter(b, a, x, axis, zi)
TypeError: array cannot be safely cast to required type

======================================================================
ERROR: test_linsolve.TestSplu.test_lu_refcount
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py",
line 186, in runTest
    self.test(*self.arg)
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py",
line 122, in test_lu_refcount
    lu = splu(a_)
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py",
line 173, in splu
    ilu=False, options=_options)
RuntimeError: Factor is exactly singular

======================================================================
ERROR: test_linsolve.TestSplu.test_spilu_smoketest
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py",
line 186, in runTest
    self.test(*self.arg)
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py",
line 60, in test_spilu_smokete
st
    lu = spilu(self.A, drop_tol=1e-2, fill_factor=5)
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py",
line 245, in spilu
    ilu=True, options=_options)
RuntimeError: Factor is exactly singular

======================================================================
ERROR: test_linsolve.TestSplu.test_splu_basic
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py",
line 186, in runTest
    self.test(*self.arg)
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py",
line 87, in test_splu_basic
    lu = splu(a_)
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py",
line 173, in splu
    ilu=False, options=_options)
RuntimeError: Factor is exactly singular

======================================================================
ERROR: test_linsolve.TestSplu.test_splu_perm
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py",
line 186, in runTest
    self.test(*self.arg)
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py",
line 100, in test_splu_perm
    lu = splu(a_)
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py",
line 173, in splu
    ilu=False, options=_options)
RuntimeError: Factor is exactly singular

======================================================================
ERROR: test_linsolve.TestSplu.test_splu_smoketest
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py",
line 186, in runTest
    self.test(*self.arg)
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py",
line 53, in test_splu_smoketes
t
    lu = splu(self.A)
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py",
line 173, in splu
    ilu=False, options=_options)
RuntimeError: Factor is exactly singular

======================================================================
ERROR: Check that QMR works with left and right preconditioners
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\isolve\tests\test_iterative.py",
line 161, in test_leftright_p
recond
    L_solver = splu(L)
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py",
line 173, in splu
    ilu=False, options=_options)
RuntimeError: Factor is exactly singular

======================================================================
ERROR: test_preconditioner (test_lgmres.TestLGMRES)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\isolve\tests\test_lgmres.py",
line 38, in test_preconditioner
    pc = splu(Am.tocsc())
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py",
line 173, in splu
    ilu=False, options=_options)
RuntimeError: Factor is exactly singular

======================================================================
ERROR: test_mu (test_base.TestBSR)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\sparse\tests\test_base.py",
line 966, in test_mu
    D1 = A * B.T
  File "C:\Python26\lib\site-packages\numpy\matrixlib\defmatrix.py",
line 319, in __mul__
    return N.dot(self, asmatrix(other))
TypeError: array cannot be safely cast to required type

======================================================================
ERROR: test_mu (test_base.TestCSC)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\sparse\tests\test_base.py",
line 966, in test_mu
    D1 = A * B.T
  File "C:\Python26\lib\site-packages\numpy\matrixlib\defmatrix.py",
line 319, in __mul__
    return N.dot(self, asmatrix(other))
TypeError: array cannot be safely cast to required type

======================================================================
ERROR: test_mu (test_base.TestCSR)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\sparse\tests\test_base.py",
line 966, in test_mu
    D1 = A * B.T
  File "C:\Python26\lib\site-packages\numpy\matrixlib\defmatrix.py",
line 319, in __mul__
    return N.dot(self, asmatrix(other))
TypeError: array cannot be safely cast to required type

======================================================================
ERROR: test_mu (test_base.TestDIA)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\sparse\tests\test_base.py",
line 966, in test_mu
    D1 = A * B.T
  File "C:\Python26\lib\site-packages\numpy\matrixlib\defmatrix.py",
line 319, in __mul__
    return N.dot(self, asmatrix(other))
TypeError: array cannot be safely cast to required type

======================================================================
ERROR: test_mu (test_base.TestLIL)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\sparse\tests\test_base.py",
line 966, in test_mu
    D1 = A * B.T
  File "C:\Python26\lib\site-packages\numpy\matrixlib\defmatrix.py",
line 319, in __mul__
    return N.dot(self, asmatrix(other))
TypeError: array cannot be safely cast to required type

======================================================================
FAIL: test_complex (test_basic.TestLongDoubleFailure)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\fftpack\tests\test_basic.py",
line 527, in test_complex
    np.longcomplex)
AssertionError: Type <type 'numpy.complex128'> not supported but does not fail

======================================================================
FAIL: extrema 3
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\ndimage\tests\test_ndimage.py",
line 3149, in test_extrema03
    self.failUnless(numpy.all(output1[2]  == output4))
AssertionError

======================================================================
FAIL: test_lorentz (test_odr.TestODR)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\odr\tests\test_odr.py",
line 292, in test_lorentz
    3.7798193600109009e+00]),
  File "C:\Python26\lib\site-packages\numpy\testing\utils.py", line
765, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "C:\Python26\lib\site-packages\numpy\testing\utils.py", line
609, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal

(mismatch 100.0%)
 x: array([  1.00000000e+03,   1.00000000e-01,   3.80000000e+00])
 y: array([  1.43067808e+03,   1.33905090e-01,   3.77981936e+00])

======================================================================
FAIL: test_multi (test_odr.TestODR)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\odr\tests\test_odr.py",
line 188, in test_multi
    0.5101147161764654,  0.5173902330489161]),
  File "C:\Python26\lib\site-packages\numpy\testing\utils.py", line
765, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "C:\Python26\lib\site-packages\numpy\testing\utils.py", line
609, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal

(mismatch 100.0%)
 x: array([ 4. ,  2. ,  7. ,  0.4,  0.5])
 y: array([ 4.37998803,  2.43330576,  8.00288459,  0.51011472,  0.51739023])

======================================================================
FAIL: test_pearson (test_odr.TestODR)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\odr\tests\test_odr.py",
line 235, in test_pearson
    np.array([ 5.4767400299231674, -0.4796082367610305]),
  File "C:\Python26\lib\site-packages\numpy\testing\utils.py", line
765, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "C:\Python26\lib\site-packages\numpy\testing\utils.py", line
609, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal

(mismatch 100.0%)
 x: array([ 1.,  1.])
 y: array([ 5.47674003, -0.47960824])

======================================================================
FAIL: test_twodiags (test_linsolve.TestLinsolve)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py",
line 39, in test_twodiags
    assert( norm(b - Asp*x) < 10 * cond_A * eps )
AssertionError

======================================================================
FAIL: test_kdtree.test_vectorization.test_single_query
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py",
line 186, in runTest
    self.test(*self.arg)
  File "C:\Python26\lib\site-packages\scipy\spatial\tests\test_kdtree.py",
line 154, in test_single_query
    assert isinstance(i,int)
AssertionError

======================================================================
FAIL: test_data.test_boost(<Data for arccosh: acosh_data_ipp-acosh_data>,)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py",
line 186, in runTest
    self.test(*self.arg)
  File "C:\Python26\lib\site-packages\scipy\special\tests\test_data.py",
line 205, in _test_factory
    test.check(dtype=dtype)
  File "C:\Python26\lib\site-packages\scipy\special\tests\testutils.py",
line 187, in check
    assert False, "\n".join(msg)
AssertionError:
Max |adiff|: 1.77636e-15
Max |rdiff|: 1.09352e-13
Bad results for the following points (in output 0):
            1.0000014305114746 =>          0.0016914556651294794 !=
      0.0016914556651292944  (rdiff         1.093
5249113484058e-13)
             1.000007152557373 =>          0.0037822080446614169 !=
      0.0037822080446612951  (rdiff         3.222
0418006721235e-14)
            1.0000138282775879 =>           0.005258943946801071 !=
      0.0052589439468011014  (rdiff         5.772
5773723182603e-15)
            1.0000171661376953 =>          0.0058593666181291238 !=
      0.0058593666181292027  (rdiff         1.347
0725302071254e-14)
            1.0000600814819336 =>            0.01096183199218881 !=
       0.010961831992188852  (rdiff         3.798
0296955025714e-15)
            1.0001168251037598 =>           0.015285472131830317 !=
       0.015285472131830425  (rdiff         7.036
2795851489781e-15)
            1.0001487731933594 =>           0.017249319093529933 !=
       0.017249319093529877  (rdiff         3.218
1647826365358e-15)
            1.0003981590270996 =>           0.028218171738655599 !=
       0.028218171738655373  (rdiff         7.991
8023735059643e-15)
             1.000638484954834 =>           0.035732814682314498 !=
       0.035732814682314568  (rdiff         1.941
8828227213605e-15)
            1.0010714530944824 =>           0.046287402472878984 !=
       0.046287402472878776  (rdiff         4.497
2672043800306e-15)
            1.0049939155578613 =>           0.099897593086028066 !=
       0.099897593086027803  (rdiff         2.639
4826962588157e-15)
                1.024169921875 =>            0.21942279004958387 !=
        0.21942279004958354  (rdiff         1.517
9230348510424e-15)

======================================================================
FAIL: test_data.test_boost(<Data for arctanh: atanh_data_ipp-atanh_data>,)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py",
line 186, in runTest
    self.test(*self.arg)
  File "C:\Python26\lib\site-packages\scipy\special\tests\test_data.py",
line 205, in _test_factory
    test.check(dtype=dtype)
  File "C:\Python26\lib\site-packages\scipy\special\tests\testutils.py",
line 187, in check
    assert False, "\n".join(msg)
AssertionError:
Max |adiff|: 6.39488e-12
Max |rdiff|: 1.01982e-12
Bad results for the following points (in output 0):
          -0.99999284744262695 =>            -6.2705920974721474 !=
        -6.2705920974657525  (rdiff         1.019
8214973073088e-12)
          -0.99998283386230469 =>             -5.832855225376532 !=
         -5.832855225378502  (rdiff         3.377
3849320373679e-13)

----------------------------------------------------------------------
Ran 4410 tests in 29.842s

FAILED (KNOWNFAIL=11, SKIP=38, errors=16, failures=9)
<nose.result.TextTestResult run=4410 errors=16 failures=9>
>>>


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