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<div>Installed biopython 1.7 running under anaconda installed python 2.7.14</div>
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<div>The first two failures involve a URL conflict where one has http, and the other has https.</div>
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<div>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.</div>
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<div>$ cd ../../biopython-1.70/Tests/</div>
<div>$ python run_tests.py</div>
<div>Python version: 2.7.14 |Anaconda, Inc.| (default, Dec 7 2017, 17:05:42) </div>
<div>[GCC 7.2.0]</div>
<div>Operating system: posix linux2</div>
<div>...</div>
<div>Bio.SVDSuperimposer docstring test ... FAIL</div>
<div>FAIL: test_prodoc_html (test_ExPASy.ExPASyOnlineTests)</div>
<div>Traceback (most recent call last):</div>
<div> File "~/build/biopython-1.70/Tests/test_ExPASy.py", line 51, in test_prodoc_html</div>
<div> 'http://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry?PDOC00001')</div>
<div>AssertionError: 'https://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry?PDOC00001' != 'http://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry?PDOC00001'</div>
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<div>FAIL: test_prosite_html (test_ExPASy.ExPASyOnlineTests)</div>
<div>Traceback (most recent call last):</div>
<div> File "~/build/biopython-1.70/Tests/test_ExPASy.py", line 43, in test_prosite_html</div>
<div> 'http://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry?PS00001')</div>
<div>AssertionError: 'https://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry?PS00001' != 'http://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry?PS00001'</div>
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<div>FAIL: Record (Bio.Affy.CelFile)</div>
<div>Doctest: Bio.Affy.CelFile.Record</div>
<div>Traceback (most recent call last):</div>
<div> File "~/anaconda2/lib/python2.7/doctest.py", line 2226, in runTest</div>
<div> raise self.failureException(self.format_failure(new.getvalue()))</div>
<div>AssertionError: Failed doctest test for Bio.Affy.CelFile.Record</div>
<div> File "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/Affy/CelFile.py", line 35, in Record</div>
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<div>File "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/Affy/CelFile.py", line 46, in Bio.Affy.CelFile.Record</div>
<div>Failed example:</div>
<div> print(c.intensities)</div>
<div>Expected:</div>
<div> [[ 234. 170. 22177. 164. 22104.]</div>
<div> [ 188. 188. 21871. 168. 21883.]</div>
<div> [ 188. 193. 21455. 198. 21300.]</div>
<div> [ 188. 182. 21438. 188. 20945.]</div>
<div> [ 193. 20370. 174. 20605. 168.]]</div>
<div>Got:</div>
<div> [[ 234. 170. 22177. 164. 22104.]</div>
<div> [ 188. 188. 21871. 168. 21883.]</div>
<div> [ 188. 193. 21455. 198. 21300.]</div>
<div> [ 188. 182. 21438. 188. 20945.]</div>
<div> [ 193. 20370. 174. 20605. 168.]]</div>
<div>File "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/Affy/CelFile.py", line 52, in Bio.Affy.CelFile.Record</div>
<div>Failed example:</div>
<div> print(c.stdevs)</div>
<div>Expected:</div>
<div> [[ 24. 34.5 2669. 19.7 3661.2]</div>
<div> [ 29.8 29.8 2795.9 67.9 2792.4]</div>
<div> [ 29.8 88.7 2976.5 62. 2914.5]</div>
<div> [ 29.8 76.2 2759.5 49.2 2762. ]</div>
<div> [ 38.8 2611.8 26.6 2810.7 24.1]]</div>
<div>Got:</div>
<div> [[ 24. 34.5 2669. 19.7 3661.2]</div>
<div> [ 29.8 29.8 2795.9 67.9 2792.4]</div>
<div> [ 29.8 88.7 2976.5 62. 2914.5]</div>
<div> [ 29.8 76.2 2759.5 49.2 2762. ]</div>
<div> [ 38.8 2611.8 26.6 2810.7 24.1]]</div>
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<div>======================================================================</div>
<div>FAIL: SVDSuperimposer (Bio.SVDSuperimposer)</div>
<div>Doctest: Bio.SVDSuperimposer.SVDSuperimposer</div>
<div>----------------------------------------------------------------------</div>
<div>Traceback (most recent call last):</div>
<div> File "~/anaconda2/lib/python2.7/doctest.py", line 2226, in runTest</div>
<div> raise self.failureException(self.format_failure(new.getvalue()))</div>
<div>AssertionError: Failed doctest test for Bio.SVDSuperimposer.SVDSuperimposer</div>
<div> File "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/__init__.py", line 24, in SVDSuperimposer</div>
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<div>File "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/__init__.py", line 83, in Bio.SVDSuperimposer.SVDSuperimposer</div>
<div>Failed example:</div>
<div> print(y_on_x1)</div>
<div>Expected:</div>
<div> [[ 5.17e+01 -1.90e+00 5.01e+01]</div>
<div> [ 5.04e+01 -1.23e+00 5.06e+01]</div>
<div> [ 5.07e+01 -4.16e-02 5.15e+01]</div>
<div> [ 5.02e+01 -1.94e-02 5.29e+01]]</div>
<div>Got:</div>
<div> [[ 5.17e+01 -1.90e+00 5.01e+01]</div>
<div> [ 5.04e+01 -1.23e+00 5.06e+01]</div>
<div> [ 5.07e+01 -4.16e-02 5.15e+01]</div>
<div> [ 5.02e+01 -1.94e-02 5.29e+01]]</div>
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<div>File "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/__init__.py", line 88, in Bio.SVDSuperimposer.SVDSuperimposer</div>
<div>Failed example:</div>
<div> print(y_on_x2)</div>
<div>Expected:</div>
<div> [[ 5.17e+01 -1.90e+00 5.01e+01]</div>
<div> [ 5.04e+01 -1.23e+00 5.06e+01]</div>
<div> [ 5.07e+01 -4.16e-02 5.15e+01]</div>
<div> [ 5.02e+01 -1.94e-02 5.29e+01]]</div>
<div>Got:</div>
<div> [[ 5.17e+01 -1.90e+00 5.01e+01]</div>
<div> [ 5.04e+01 -1.23e+00 5.06e+01]</div>
<div> [ 5.07e+01 -4.16e-02 5.15e+01]</div>
<div> [ 5.02e+01 -1.94e-02 5.29e+01]]</div>
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<div>----------------------------------------------------------------------</div>
<div>Ran 274 tests in 520.026 seconds</div>
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<div>FAILED (failures = 3)</div>
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<div>-- </div>
<div>Gregory Dougherty</div>
<div>Sr. Analyst/Programmer</div>
<div>Information Technology</div>
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