[Numpy-discussion] numpy.test error: test_hdquantiles

Charles R Harris charlesr.harris@gmail....
Sun May 25 16:52:26 CDT 2008


On Sun, May 25, 2008 at 3:35 PM, Joshua Lippai <discerptor@gmail.com> wrote:

> I seem to be getting a few errors and failures with the current numpy
> SVN (1.2.0.dev5236). I get this output with numpy.test(1,10):
>
> ERROR: Ticket #396
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/tests/test_regression.py",
> line 602, in check_poly1d_nan_roots
>    self.failUnlessRaises(np.linalg.LinAlgError,getattr,p,"r")
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/unittest.py",
> line 320, in failUnlessRaises
>    callableObj(*args, **kwargs)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/polynomial.py",
> line 661, in __getattr__
>    return roots(self.coeffs)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/polynomial.py",
> line 124, in roots
>    roots = _eigvals(A)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/polynomial.py",
> line 40, in _eigvals
>    return eigvals(arg)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/decomp.py",
> line 478, in eigvals
>    return eig(a,b=b,left=0,right=0,overwrite_a=overwrite_a)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/decomp.py",
> line 150, in eig
>    a1 = asarray_chkfinite(a)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/function_base.py",
> line 527, in asarray_chkfinite
>    raise ValueError, "array must not contain infs or NaNs"
> ValueError: array must not contain infs or NaNs
>
> ======================================================================
> ERROR: Ticket #396
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/tests/test_regression.py",
> line 602, in check_poly1d_nan_roots
>    self.failUnlessRaises(np.linalg.LinAlgError,getattr,p,"r")
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/unittest.py",
> line 320, in failUnlessRaises
>    callableObj(*args, **kwargs)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/polynomial.py",
> line 661, in __getattr__
>    return roots(self.coeffs)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/polynomial.py",
> line 124, in roots
>    roots = _eigvals(A)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/polynomial.py",
> line 37, in _eigvals
>    return eigvals(arg)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/decomp.py",
> line 478, in eigvals
>    return eig(a,b=b,left=0,right=0,overwrite_a=overwrite_a)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/decomp.py",
> line 150, in eig
>    a1 = asarray_chkfinite(a)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/function_base.py",
> line 527, in asarray_chkfinite
>    raise ValueError, "array must not contain infs or NaNs"
> ValueError: array must not contain infs or NaNs
>
> ======================================================================
> ERROR: test_hdquantiles (numpy.ma.tests.test_morestats.TestQuantiles)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/ma/tests/test_morestats.py",
> line 97, in test_hdquantiles
>    hdq = hdquantiles_sd(data,[0.25, 0.5, 0.75])
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/ma/morestats.py",
> line 168, in hdquantiles_sd
>    result = _hdsd_1D(data.compressed(), p)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/ma/morestats.py",
> line 144, in _hdsd_1D
>    xsorted = numpy.sort(data.compressed())
> AttributeError: 'numpy.ndarray' object has no attribute 'compressed'
>
> ======================================================================
> FAIL: Tests the Marits-Jarrett estimator
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/ma/tests/test_morestats.py",
> line 36, in test_mjci
>    assert_almost_equal(mjci(data),[55.76819,45.84028,198.8788],5)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/ma/testutils.py",
> line 134, in assert_almost_equal
>    return assert_array_almost_equal(actual, desired, decimal, err_msg)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/ma/testutils.py",
> line 227, in assert_array_almost_equal
>    header='Arrays are not almost equal')
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/ma/testutils.py",
> line 193, in assert_array_compare
>    assert cond, msg
> AssertionError:
> Arrays are not almost equal
>
> (mismatch 33.3333333333%)
>  x: array([  55.76818915,   45.84027529,  198.8787528 ])
>  y: array([  55.76819,   45.84028,  198.8788 ])
>
> ======================================================================
> FAIL: Test quantiles 1D - w/ mask.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/ma/tests/test_mstats.py",
> line 61, in test_1d_mask
>    [24.833333, 50.0, 75.166666])
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/ma/testutils.py",
> line 134, in assert_almost_equal
>    return assert_array_almost_equal(actual, desired, decimal, err_msg)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/ma/testutils.py",
> line 227, in assert_array_almost_equal
>    header='Arrays are not almost equal')
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/ma/testutils.py",
> line 193, in assert_array_compare
>    assert cond, msg
> AssertionError:
> Arrays are not almost equal
>
> (mismatch 66.6666666667%)
>  x: array([ 24.83333333,  50.        ,  75.16666667])
>  y: array([ 24.833333,  50.      ,  75.166666])
>
> ----------------------------------------------------------------------
> Ran 1301 tests in 1.501s
>
> FAILED (failures=2, errors=3)
> <unittest._TextTestResult run=1301 errors=3 failures=2>
> >>> numpy.__version__
> '1.2.0.dev5236'
> >>> scipy.__version__
> '0.7.0.dev4386'
>
> I get that the failures are just NumPy being anal about the accuracy
> and rounding habits, but the errors concern me. The first two are the
> result of a ticket that's only supposed to pop up when SciPy isn't
> installed (which it is, and I even imported it before running the
> test). I assume those will go away by some strange voodoo magic on
> their own eventually because this has happened to me before with that
> particular ticket. The third error concerns me, though. Is anyone else
> getting an error with test_hdquantiles?
> ______


Try deleting site-packages/numpy and the build directory and reinstalling.
The current default testing level is greater than it was and some old tests
may be hanging about. What platform are you on? I get 1353 tests run, which
is quite a bit larger than  the 1301 your output shows.

Chuck
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