[SciPy-dev] ERROR: Tests pdist(X, 'cosine') on the Iris data set.
Nils Wagner
nwagner at iam.uni-stuttgart.de
Wed Jun 4 05:46:33 EDT 2008
On Wed, 04 Jun 2008 01:12:55 -0700
Damian Eads <eads at soe.ucsc.edu> wrote:
> Nils Wagner wrote:
>> Hi All,
>>
>> Can someone reproduce the following error with
>>>>> scipy.__version__
>> '0.7.0.dev4411'
>>>>> numpy.__version__
>> '1.2.0.dev5252'
>>
>> ======================================================================
>> ERROR: Tests pdist(X, 'cosine') on the Iris data set.
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File
>> "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py",
>> line 264, in test_pdist_cosine_iris
>> Y_test1 = pdist(X, 'cosine')
>> File
>> "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/cluster/hierarchy.py",
>> line 1478, in pdist
>> dm = squareform(dm)
>> File
>> "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/cluster/hierarchy.py",
>> line 766, in squareform
>> raise ValueError('The distance matrix array must be
>> symmetrical.')
>> ValueError: The distance matrix array must be
>>symmetrical.
>>
>> Nils
>
> Sorry about that. This is a fairly new test in a new
>module so I'm still
> ironing out numerical differences between architectures.
>Although, I was
> not able to reproduce the error, I believe reverting
>back to the C
> implementation of pdist(*, 'cosine') instead of the
>vectorized version
> might fix the problem. I just committed the change
>(4412).
>
> Damian
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> Scipy-dev at scipy.org
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Damian,
Thank you. Works fine for me now.
Cheers,
Nils
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