[Biopython] Getting apparently spurious errors when running tests

[Dougherty, Gregory T., M.S.]

Installed biopython 1.7 running under anaconda installed python 2.7.14

The first two failures involve a URL conflict where one has http, and the other has https.

The last four come from arrays, and the only difference I see is the “expected” have two spaces between each number, and the “actual” have only one space.

$ 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)
Traceback (most recent call last):
  File "~/build/biopython-1.70/Tests/test_ExPASy.py", line 51, in test_prodoc_html
    'http://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry?PDOC00001')
AssertionError: 'https://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry?PDOC00001' != 'http://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry?PDOC00001'

FAIL: test_prosite_html (test_ExPASy.ExPASyOnlineTests)
Traceback (most recent call last):
  File "~/build/biopython-1.70/Tests/test_ExPASy.py", line 43, in test_prosite_html
    'http://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry?PS00001')
AssertionError: 'https://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry?PS00001' != 'http://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry?PS00001'

FAIL: Record (Bio.Affy.CelFile)
Doctest: Bio.Affy.CelFile.Record
Traceback (most recent call last):
  File "~/anaconda2/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for Bio.Affy.CelFile.Record
  File "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/Affy/CelFile.py", line 35, in Record

File "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/Affy/CelFile.py", line 46, in Bio.Affy.CelFile.Record
Failed example:
    print(c.intensities)
Expected:
    [[   234.    170.  22177.    164.  22104.]
     [   188.    188.  21871.    168.  21883.]
     [   188.    193.  21455.    198.  21300.]
     [   188.    182.  21438.    188.  20945.]
     [   193.  20370.    174.  20605.    168.]]
Got:
    [[  234.   170. 22177.   164. 22104.]
     [  188.   188. 21871.   168. 21883.]
     [  188.   193. 21455.   198. 21300.]
     [  188.   182. 21438.   188. 20945.]
     [  193. 20370.   174. 20605.   168.]]
File "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/Affy/CelFile.py", line 52, in Bio.Affy.CelFile.Record
Failed example:
    print(c.stdevs)
Expected:
    [[   24.     34.5  2669.     19.7  3661.2]
     [   29.8    29.8  2795.9    67.9  2792.4]
     [   29.8    88.7  2976.5    62.   2914.5]
     [   29.8    76.2  2759.5    49.2  2762. ]
     [   38.8  2611.8    26.6  2810.7    24.1]]
Got:
    [[  24.    34.5 2669.    19.7 3661.2]
     [  29.8   29.8 2795.9   67.9 2792.4]
     [  29.8   88.7 2976.5   62.  2914.5]
     [  29.8   76.2 2759.5   49.2 2762. ]
     [  38.8 2611.8   26.6 2810.7   24.1]]


======================================================================
FAIL: SVDSuperimposer (Bio.SVDSuperimposer)
Doctest: Bio.SVDSuperimposer.SVDSuperimposer
----------------------------------------------------------------------
Traceback (most recent call last):
  File "~/anaconda2/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for Bio.SVDSuperimposer.SVDSuperimposer
  File "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/__init__.py", line 24, in SVDSuperimposer

File "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/__init__.py", line 83, in Bio.SVDSuperimposer.SVDSuperimposer
Failed example:
    print(y_on_x1)
Expected:
    [[  5.17e+01  -1.90e+00   5.01e+01]
     [  5.04e+01  -1.23e+00   5.06e+01]
     [  5.07e+01  -4.16e-02   5.15e+01]
     [  5.02e+01  -1.94e-02   5.29e+01]]
Got:
    [[ 5.17e+01 -1.90e+00  5.01e+01]
     [ 5.04e+01 -1.23e+00  5.06e+01]
     [ 5.07e+01 -4.16e-02  5.15e+01]
     [ 5.02e+01 -1.94e-02  5.29e+01]]

File "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/__init__.py", line 88, in Bio.SVDSuperimposer.SVDSuperimposer
Failed example:
    print(y_on_x2)
Expected:
    [[  5.17e+01  -1.90e+00   5.01e+01]
     [  5.04e+01  -1.23e+00   5.06e+01]
     [  5.07e+01  -4.16e-02   5.15e+01]
     [  5.02e+01  -1.94e-02   5.29e+01]]
Got:
    [[ 5.17e+01 -1.90e+00  5.01e+01]
     [ 5.04e+01 -1.23e+00  5.06e+01]
     [ 5.07e+01 -4.16e-02  5.15e+01]
     [ 5.02e+01 -1.94e-02  5.29e+01]]


----------------------------------------------------------------------
Ran 274 tests in 520.026 seconds

FAILED (failures = 3)

--
Gregory Dougherty
Sr. Analyst/Programmer
Information Technology

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