samedi 1 octobre 2016

biopython installation test fail: ERROR: test_fetch_xml_schemas (test_Entrez_online.EntrezOnlineCase)

Hi,

I'm trying to test the installation of biopython on my Mac and used this command:

sudo python3 setup.py test

Everything is fine except this error message:

    ERROR: test_fetch_xml_schemas (test_Entrez_online.EntrezOnlineCase)
    Traceback (most recent call last):
        File "/Users/zhouyang/biopython/Tests/test_Entrez_online.py", line 205, in test_fetch_xml_schemas
             records = list(Entrez.parse(handle))
        File "/Users/zhouyang/biopython/build/lib.macosx-10.6-intel-3.5/Bio/Entrez/Parser.py", line 267, in parse
             raise CorruptedXMLError("Premature end of XML stream")
    Bio.Entrez.Parser.CorruptedXMLError: Failed to parse the XML data (Premature end of XML stream). Please make sure that the input data are not corrupted.

Also, during the test, these results shows that test_Entrez.online failed.

    test_Entrez ... ok
    test_Entrez_online ... FAIL
    test_Entrez_parser ... ok
    test_Enzyme ... ok

I'm using OS X EI capitan 10.11.6 on Mac, I have python 2.7 and 3.5.2 installed and running python3 when installing biopython and related packages.

Any idea what's going wrong, please?

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