[SciPy-User] test issues with 0.10

Paul Anton Letnes paul.anton.letnes@gmail....
Tue Nov 15 04:04:23 CST 2011


I have now built netlib BLAS+LAPACK (liblapack.a and libblas.a), and linked against these when building. Most tests pass, but there are still 16 failures. I'm not sure whether this is known, so I am posting it here in case it is of any interest.

Paul

i-courant ~/src % python -c 'import scipy; scipy.test(verbose=1)'
Running unit tests for scipy
NumPy version 1.6.1
NumPy is installed in /usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy
SciPy version 0.10.0
SciPy is installed in /usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy
Python version 2.7.2 (default, Oct  9 2011, 18:03:13) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
nose version 1.1.2
...................................................................................................................................................../usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/cluster/vq.py:588: UserWarning: One of the clusters is empty. Re-run kmean with a different initialization.
  warnings.warn("One of the clusters is empty. "
.......................................................................K............................................................................................................/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/interpolate/fitpack2.py:674: 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)
....../usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/interpolate/fitpack2.py:605: 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....../usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/core/numeric.py:1920: RuntimeWarning: invalid value encountered in absolute
  return all(less_equal(absolute(x-y), atol + rtol * absolute(y)))
............................................................................................................................................................................................................................................................................................................................................................................................................................................/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/io/wavfile.py:31: WavFileWarning: Unfamiliar format bytes
  warnings.warn("Unfamiliar format bytes", WavFileWarning)
/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/io/wavfile.py:121: WavFileWarning: chunk not understood
  warnings.warn("chunk not understood", WavFileWarning)
....................................................................................F..FF......................................................................................................................................SSSSSS......SSSSSS......SSSS.....................FFF.........................................F....FF.......S............................................................................................................................................................................................................................................................K......................................................................................................................................................................................................SSSSS............S........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSSSSSSS.........../usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py:63: UserWarning: Single-precision types in `eigs` and `eighs` are not supported on the OSX platform currently. Double precision routines are used instead.
  warnings.warn("Single-precision types in `eigs` and `eighs` "
....F.F.....................F...........F.F..............................................................................................F........................F.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K...............................................................K...........................................................................................................................................................KK.............................................................................................................................................................................................................................................................................................................................................................................................................................................K.K.............................................................................................................................................................................................................................................................................................................................................................................................K........K..............SSSSSSS..........................................................................................................................................................S.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 58, in test_asum
    assert_almost_equal(f([3,-4,5]),12)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 12

======================================================================
FAIL: test_dot (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 67, in test_dot
    assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: -9

======================================================================
FAIL: test_nrm2 (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 78, in test_nrm2
    assert_almost_equal(f([3,-4,5]),math.sqrt(50))
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 7.0710678118654755

======================================================================
FAIL: test_basic.TestNorm.test_overflow
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py", line 581, in test_overflow
    assert_almost_equal(norm(a), a)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 452, in assert_almost_equal
    return assert_array_almost_equal(actual, desired, decimal, err_msg)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 800, in assert_array_almost_equal
    header=('Arrays are not almost equal to %d decimals' % decimal))
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals

(mismatch 100.0%)
 x: array(-0.0)
 y: array([  1.00000002e+20], dtype=float32)

======================================================================
FAIL: test_basic.TestNorm.test_stable
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py", line 586, in test_stable
    assert_almost_equal(norm(a) - 1e4, 0.5)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: -10000.0
 DESIRED: 0.5

======================================================================
FAIL: test_basic.TestNorm.test_types
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py", line 568, in test_types
    assert_allclose(norm(x), np.sqrt(14), rtol=tol)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
    verbose=verbose, header=header)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Not equal to tolerance rtol=2.38419e-06, atol=0

(mismatch 100.0%)
 x: array(1.0842021724855044e-19)
 y: array(3.7416573867739413)

======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 99, in test_asum
    assert_almost_equal(f([3,-4,5]),12)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 12

======================================================================
FAIL: test_dot (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 109, in test_dot
    assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: -9

======================================================================
FAIL: test_nrm2 (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 127, in test_nrm2
    assert_almost_equal(f([3,-4,5]),math.sqrt(50))
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 7.0710678118654755

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
    verbose=verbose, header=header)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=normal
(mismatch 100.0%)
 x: array([[ 0.23815642,  0.1763755 ],
       [-0.10785346, -0.32103487],
       [ 0.12468303, -0.11230416],...
 y: array([[ 0.23815642,  0.24814051],
       [-0.10785347, -0.15634772],
       [ 0.12468302,  0.05671416],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
    verbose=verbose, header=header)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=cayley
(mismatch 100.0%)
 x: array([[ 0.23815693, -0.33630507],
       [-0.10785286,  0.02168   ],
       [ 0.12468344, -0.11036437],...
 y: array([[ 0.23815643, -0.2405392 ],
       [-0.10785349,  0.14390968],
       [ 0.12468311, -0.04574991],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LA', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
    verbose=verbose, header=header)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=normal
(mismatch 100.0%)
 x: array([[  28.80129188,   -0.6379945 ],
       [  34.79312355,    0.27066791],
       [-270.23255444,    0.4851834 ],...
 y: array([[  3.93467650e+03,  -6.37994494e-01],
       [  3.90913859e+03,   2.70667916e-01],
       [ -3.62176382e+04,   4.85183382e-01],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'SA', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
    verbose=verbose, header=header)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=SA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=normal
(mismatch 100.0%)
 x: array([[ 0.26260981,  0.23815559],
       [-0.09760907, -0.10785484],
       [ 0.06149647,  0.12468203],...
 y: array([[ 0.23744165,  0.2381564 ],
       [-0.13633069, -0.10785359],
       [ 0.03132561,  0.12468301],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'SA', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
    verbose=verbose, header=header)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=SA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=cayley
(mismatch 100.0%)
 x: array([[ 0.29524244, -0.2381569 ],
       [-0.08169955,  0.10785299],
       [ 0.06645597, -0.12468332],...
 y: array([[ 0.24180251, -0.23815646],
       [-0.14191195,  0.10785349],
       [ 0.03568392, -0.12468307],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <gen-symmetric>, 'f', 2, 'SM', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'buckling')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
    verbose=verbose, header=header)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:general, typ=f, which=SM, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=buckling
(mismatch 100.0%)
 x: array([[-0.10940548,  0.01676016],
       [-0.07154097,  0.4628113 ],
       [ 0.06895222,  0.49206394],...
 y: array([[-0.10940547,  0.05459438],
       [-0.07154103,  0.31407543],
       [ 0.06895217,  0.37578294],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <gen-symmetric>, 'f', 2, 'SA', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
    verbose=verbose, header=header)
  File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:general, typ=f, which=SA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=cayley
(mismatch 100.0%)
 x: array([[-0.4404992 , -0.01935683],
       [-0.25650678, -0.11053132],
       [-0.36893024, -0.13223556],...
 y: array([[-0.44017013, -0.0193569 ],
       [-0.25525379, -0.11053158],
       [-0.36818443, -0.13223571],...

----------------------------------------------------------------------
Ran 5093 tests in 50.678s

FAILED (KNOWNFAIL=12, SKIP=42, failures=16)




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