[Biopython] Getting apparently spurious errors when running tests
Dougherty, Gregory T., M.S.
Dougherty.Gregory at mayo.edu
Tue Feb 20 00:28:07 UTC 2018
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 "/home/tu04809/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 "/home/tu04809/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 "/home/tu04809/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 "/home/tu04809/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/Affy/CelFile.py", line 35, in Record
----------------------------------------------------------------------
File "/home/tu04809/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 "/home/tu04809/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 "/home/tu04809/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 "/home/tu04809/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/__init__.py", line 24, in SVDSuperimposer
----------------------------------------------------------------------
File "/home/tu04809/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 "/home/tu04809/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
Information Technology
(507) 284-8493 | dougherty.gregory at mayo.edu<mailto:dougherty.gregory at mayo.edu>
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