[SciPy-Dev] Errors with numpy-devel
Nils Wagner
nils106 at googlemail.com
Tue Apr 15 15:19:32 EDT 2014
>>> from scipy import stats
>>> stats.test()
Running unit tests for scipy.stats
NumPy version 1.9.0.dev-61c699e
NumPy is installed in /home/nils/local/lib64/python2.7/site-packages/numpy
SciPy version 0.15.0.dev-87df1db
SciPy is installed in /home/nils/local/lib64/python2.7/site-packages/scipy
Python version 2.7.3 (default, Apr 14 2012, 08:58:41) [GCC]
nose version 1.3.1
...
======================================================================
ERROR: test_gmean (test_mstats_basic.TestCompareWithStats)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
line 763, in test_gmean
rm = stats.mstats.gmean(abs(xm))
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/stats.py", line
516, in gmean
log_a = np.log(a)
File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py",
line 2837, in __array_wrap__
d = filled(domain(*args), True)
File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py",
line 795, in __call__
return umath.less_equal(x, self.critical_value)
RuntimeWarning: invalid value encountered in less_equal
======================================================================
ERROR: test_hmean (test_mstats_basic.TestCompareWithStats)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
line 775, in test_hmean
rm = stats.mstats.hmean(abs(xm))
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/stats.py", line
562, in hmean
if np.all(a > 0): # Harmonic mean only defined if greater than zero
RuntimeWarning: invalid value encountered in greater
======================================================================
ERROR: test_tmax (test_mstats_basic.TestCompareWithStats)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
line 908, in test_tmax
stats.mstats.tmax(xm,2.), 10)
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py",
line 1383, in tmax
am = trima(a, (None, upperlimit), (False, inclusive))
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py",
line 1018, in trima
condition |= (a > upper_lim)
RuntimeWarning: invalid value encountered in greater
======================================================================
ERROR: test_tmin (test_mstats_basic.TestCompareWithStats)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
line 919, in test_tmin
stats.mstats.tmin(xm,lowerlimit=-1.), 10)
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py",
line 1376, in tmin
am = trima(a, (lowerlimit, None), (inclusive, False))
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py",
line 1013, in trima
condition |= (a < lower_lim)
RuntimeWarning: invalid value encountered in less
======================================================================
ERROR: test_tsem (test_mstats_basic.TestCompareWithStats)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
line 958, in test_tsem
stats.mstats.tsem(xm,limits=(-2.,2.)),
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py",
line 1393, in tsem
am = trima(a.ravel(), limits, inclusive)
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py",
line 1013, in trima
condition |= (a < lower_lim)
RuntimeWarning: invalid value encountered in less
======================================================================
ERROR: test_zmap (test_mstats_basic.TestCompareWithStats)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
line 927, in test_zmap
zm = stats.mstats.zmap(xm,ym)
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/stats.py", line
2063, in zmap
return (scores - mns) / sstd
File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py",
line 3735, in __truediv__
return true_divide(self, other)
File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py",
line 1089, in __call__
m |= filled(domain(da, db), True)
File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py",
line 783, in __call__
return umath.absolute(a) * self.tolerance >= umath.absolute(b)
RuntimeWarning: invalid value encountered in greater_equal
======================================================================
FAIL: test_example1a (test_morestats.TestAndersonKSamp)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_morestats.py",
line 97, in test_example1a
midrank=False)
File
"/home/nils/local/lib64/python2.7/site-packages/numpy/testing/utils.py",
line 1593, in assert_warns
% func.__name__)
AssertionError: No warning raised when calling anderson_ksamp
======================================================================
FAIL: test_tmean (test_mstats_basic.TestCompareWithStats)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
line 901, in test_tmean
assert_equal(stats.tmean(x),stats.mstats.tmean(xm))
File
"/home/nils/local/lib64/python2.7/site-packages/numpy/ma/testutils.py",
line 100, in assert_equal
raise AssertionError(msg)
AssertionError:
Items are not equal:
ACTUAL: 0.040175456835823721
DESIRED: 0.040175456835823714
======================================================================
FAIL: test_trim (test_mstats_basic.TestTrimming)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
line 274, in test_trim
assert_equal(trimx._mask.ravel(),[1]*20+[0]*70+[1]*20)
File
"/home/nils/local/lib64/python2.7/site-packages/numpy/ma/testutils.py",
line 123, in assert_equal
return assert_array_equal(actual, desired, err_msg)
File
"/home/nils/local/lib64/python2.7/site-packages/numpy/ma/testutils.py",
line 196, in assert_array_equal
header='Arrays are not equal')
File
"/home/nils/local/lib64/python2.7/site-packages/numpy/ma/testutils.py",
line 189, in assert_array_compare
verbose=verbose, header=header)
File
"/home/nils/local/lib64/python2.7/site-packages/numpy/testing/utils.py",
line 660, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not equal
(mismatch 9.09090909091%)
x: array([ True, True, True, True, True, True, True, True, True,
True, True, True, True, True, True, True, True, True,
True, True, False, False, False, False, False, False, False,...
y: array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0,
0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0,...
----------------------------------------------------------------------
Ran 1957 tests in 50.047s
FAILED (KNOWNFAIL=4, SKIP=3, errors=6, failures=3)
<nose.result.TextTestResult run=1957 errors=6 failures=3>
On Sun, Apr 13, 2014 at 10:58 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>
>
>
> On Sun, Apr 13, 2014 at 7:42 AM, Charles R Harris <
> charlesr.harris at gmail.com> wrote:
>
>> Hi All,
>>
>> I get 75 errors and 3 failures when testing against current numpy on my
>> machine. Most of the errors are due to either the deprecation of the binary
>> '-' operator for booleans or to the deprecation of double ellipsis for
>> indexing, i.e., '(..., ...)' . The remainder look like two numerical
>> precision problems and one I can't immediately identify.
>>
>> The main question I have is what is the best way to deal with the
>> deprecations?
>>
>
> Fix them? It's not that much work; I'd like to still get that into 0.14.0
> if possible. Will have a look.
>
> The QHull test I've seen fail randomly on various platforms, it has a real
> issue. The other two look like the tests need adapting.
>
> Ralf
>
>
>>
>> FAIL: test_lsmr.TestLSMR.testBidiagonalA
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in
>> runTest
>> self.test(*self.arg)
>> File
>> "/home/charris/.local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/tests/test_lsmr.py",
>> line 60, in testBidiagonalA
>> self.assertCompatibleSystem(A,xtrue)
>> File
>> "/home/charris/.local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/tests/test_lsmr.py",
>> line 40, in assertCompatibleSystem
>> assert_almost_equal(norm(x - xtrue), 0, 6)
>> File
>> "/home/charris/.local/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 486, in assert_almost_equal
>> raise AssertionError(_build_err_msg())
>> AssertionError:
>> Arrays are not almost equal to 6 decimals
>> ACTUAL: 6.048630163037888e-07
>> DESIRED: 0
>>
>> ======================================================================
>> FAIL: test_qhull.TestUtilities.test_degenerate_barycentric_transforms
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in
>> runTest
>> self.test(*self.arg)
>> File
>> "/home/charris/.local/lib/python2.7/site-packages/numpy/testing/decorators.py",
>> line 146, in skipper_func
>> return f(*args, **kwargs)
>> File
>> "/home/charris/.local/lib/python2.7/site-packages/scipy/spatial/tests/test_qhull.py",
>> line 296, in test_degenerate_barycentric_transforms
>> assert_(bad_count < 20, bad_count)
>> File
>> "/home/charris/.local/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 50, in assert_
>> raise AssertionError(smsg)
>> AssertionError: 20
>>
>> ======================================================================
>> FAIL: test_trim (test_mstats_basic.TestTrimming)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File
>> "/home/charris/.local/lib/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
>> line 270, in test_trim
>> assert_equal(trimx._mask.ravel(),[1]*20+[0]*70+[1]*20)
>> File
>> "/home/charris/.local/lib/python2.7/site-packages/numpy/ma/testutils.py",
>> line 123, in assert_equal
>> return assert_array_equal(actual, desired, err_msg)
>> File
>> "/home/charris/.local/lib/python2.7/site-packages/numpy/ma/testutils.py",
>> line 196, in assert_array_equal
>> header='Arrays are not equal')
>> File
>> "/home/charris/.local/lib/python2.7/site-packages/numpy/ma/testutils.py",
>> line 189, in assert_array_compare
>> verbose=verbose, header=header)
>> File
>> "/home/charris/.local/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 660, in assert_array_compare
>> raise AssertionError(msg)
>> AssertionError:
>> Arrays are not equal
>>
>> (mismatch 9.09090909091%)
>> x: array([ True, True, True, True, True, True, True, True, True,
>> True, True, True, True, True, True, True, True, True,
>> True, True, False, False, False, False, False, False, False,...
>> y: array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0,
>> 0, 0,
>> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
>> 0,
>> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
>> 0,...
>>
>> Chuck
>>
>>
>>
>> _______________________________________________
>> SciPy-Dev mailing list
>> SciPy-Dev at scipy.org
>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>
>>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
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