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

Samuel John scipy@samueljohn...
Thu Jan 26 12:41:38 CST 2012


Update:

Only 7 arpack related fails. So looks pretty good. The tests should then be marked as to be skipped, I guess.

NumPy version 1.6.1
SciPy version 0.10.0
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

:-)

Samuel


On 21.01.2012, at 13:53, Ralf Gommers wrote:

> 
> 
> On Fri, Jan 20, 2012 at 9:23 PM, Samuel John <scipy@samueljohn.de> wrote:
> Hi SciPy devs,
> 
> I just want to report the following failures. Does anybody on OSX get the same/similar?
>  
> The Arpack ones are causing problems on several platforms, they should be disabled. It's on my (way too long) TODO list.
>  
> The test_contingency failure I've seen before on OS X, but usually just once. Since I can't reproduce it I suspect it's a nose bug. The frozen_fit one I'm not sure about. Does it fail consistently for you? If so, can you run the test as standalone script and have it still failing?
>  
> Ralf
>  
>  
> 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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