[SciPy-User] SciPy 0.10: 8 failures on OS X Lion

Samuel John scipy@samueljohn...
Fri Jan 20 07:23:12 CST 2012


Hi SciPy devs, 

I just want to report the following failures. Does anybody on OSX get the same/similar?
Are they "known" ?
Should I try scipy 0.11 because they are fixed there, perhaps?
Six out of eight are related to arpack.
I have installed numpy, scipy with gfortran provided by homebrew and I set the CC, CXX to use the non-llvm compilers of the 4.2 series.


> Python 2.7.2 (default, Jan 13 2012, 15:00:18) 
> [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.1.00)] on darwin
> >>> import scipy
> >>> scipy.test()
> Running unit tests for scipy
> NumPy version 2.0.0.dev-55472ca
> NumPy is installed in /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy
> SciPy version 0.10.0
> SciPy is installed in /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy
> Python version 2.7.2 (default, Jan 13 2012, 15:00:18) [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.1.00)]
> nose version 1.1.2
> .
> .
> .
> ======================================================================
> FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM', None, 0.5, <function aslinearoperator at 0x103a58f50>, None, 'normal')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
>     self.test(*self.arg)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/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/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 1213, in assert_allclose
>     verbose=verbose, header=header)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 677, 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 0x103a58f50>, None, 'cayley')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
>     self.test(*self.arg)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/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/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 1213, in assert_allclose
>     verbose=verbose, header=header)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 677, 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 0x103a58f50>, None, 'normal')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
>     self.test(*self.arg)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/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/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 1213, in assert_allclose
>     verbose=verbose, header=header)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 677, 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 0x103a58f50>, None, 'normal')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
>     self.test(*self.arg)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/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/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 1213, in assert_allclose
>     verbose=verbose, header=header)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 677, 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 0x103a58f50>, None, 'cayley')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
>     self.test(*self.arg)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/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/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 1213, in assert_allclose
>     verbose=verbose, header=header)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 677, 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 0x103a58f50>, None, 'buckling')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
>     self.test(*self.arg)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/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/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 1213, in assert_allclose
>     verbose=verbose, header=header)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 677, 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 0x103a58f50>, None, 'cayley')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
>     self.test(*self.arg)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/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/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 1213, in assert_allclose
>     verbose=verbose, header=header)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 677, 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],...
> 
> ======================================================================
> FAIL: test_contingency.test_expected_freq
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
>     self.test(*self.arg)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/tests/test_contingency.py", line 45, in test_expected_freq
>     assert_array_equal(e, np.ones_like(observed))
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 753, in assert_array_equal
>     verbose=verbose, header='Arrays are not equal')
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 677, in assert_array_compare
>     raise AssertionError(msg)
> AssertionError: 
> Arrays are not equal
> 
> (mismatch 100.0%)
>  x: array([[[ 0.,  0.],
>         [ 0.,  0.]],
> ...
>  y: array([[[1, 1],
>         [1, 1]],
> ...
> 
> ======================================================================
> FAIL: test_distributions.test_frozen_fit_ticket_1536
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
>     self.test(*self.arg)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/tests/test_distributions.py", line 747, in test_frozen_fit_ticket_1536
>     assert_almost_equal(params, true, decimal=2)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 451, in assert_almost_equal
>     return assert_array_almost_equal(actual, desired, decimal, err_msg)
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 846, in assert_array_almost_equal
>     header=('Arrays are not almost equal to %d decimals' % decimal))
>   File "/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 677, in assert_array_compare
>     raise AssertionError(msg)
> AssertionError: 
> Arrays are not almost equal to 2 decimals
> 
> (mismatch 66.6666666667%)
>  x: array([ 1.416,  0.   ,  0.061])
>  y: array([ 0.25,  0.  ,  0.5 ])
> 
> ----------------------------------------------------------------------
> Ran 5095 tests in 54.587s
> 
> FAILED (KNOWNFAIL=12, SKIP=36, failures=9)
> <nose.result.TextTestResult run=5095 errors=0 failures=9>
> 




And some warning that look strange (at least to me):
> site-packages/scipy/spatial/__init__.py:26: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility
> site-packages/scipy/spatial/__init__.py:26: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility


cheers,
 Samuel


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