[Biopython] Getting apparently spurious errors when running tests

[Peter Cock]

Your installation would appear to be fine - these two
test failures are harmless.

Peter

(I seemed to get your email twice, no idea why though)


On Tue, Feb 20, 2018 at 6:37 PM, Dougherty, Gregory T., M.S.
<Dougherty.Gregory at mayo.edu> wrote:
> Thank you Peter.
>
> Should I take from this that my installation of BioPython is correct?
> --
> Gregory Dougherty
> Sr. Analyst/Programmer | Information Technology
> Information Technology
> (507) 284-8493 | dougherty.gregory at mayo.edu
>
>
>
> On 2/20/18, 3:46 AM, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:
>
>>Hi Gregory,
>>
>>The good news is these two issues are harmless.
>>
>>ExPASy HTTP vs HTTPS has been fixed:
>>https://github.com/biopython/biopython/pull/1428
>>
>>The second issue is white space differences in NumPy 1.14,
>>which we have not yet properly resolved:
>>
>>https://github.com/biopython/biopython/issues/1496
>>
>>Peter
>>
>>On Tue, Feb 20, 2018 at 3:52 AM, Dougherty, Gregory T., M.S.
>><Dougherty.Gregory at mayo.edu> wrote:
>>> Installed biopython 1.7 running under anaconda installed python 2.7.14
>>>
>>> $ cd ../../biopython-1.70/Tests/
>>> $ python run_tests.py
>>> Python version: 2.7.14 |Anaconda, Inc.| (default, Dec  7 2017, 17:05:42)
>>> [GCC 7.2.0]
>>> Operating system: posix linux2
>>> ...
>>> Bio.SVDSuperimposer docstring test ... FAIL
>>>======================================================================
>>>FAIL: test_prodoc_html (test_ExPASy.ExPASyOnlineTests)
>>>======================================================================
>>>FAIL: test_prosite_html (test_ExPASy.ExPASyOnlineTests)
>>>======================================================================
>>>FAIL: Record (Bio.Affy.CelFile)
>>> Doctest: Bio.Affy.CelFile.Record
>>>======================================================================
>>> FAIL: SVDSuperimposer (Bio.SVDSuperimposer)
>>> Doctest: Bio.SVDSuperimposer.SVDSuperimposer
>>>----------------------------------------------------------------------
>>> Ran 274 tests in 520.026 seconds
>>>
>>> FAILED (failures = 3)
>>>
>>> --
>>> Gregory Dougherty
>>> Sr. Analyst/Programmer
>>> Information Technology
>>>
>>>
>>> _______________________________________________
>>> Biopython mailing list  -  Biopython at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/biopython
>>
>