[Biopython-dev] Errors about installing biopython 1.61

[林行众]

2013/5/13 Peter Cock <p.j.a.cock at googlemail.com>:
> On Sun, May 12, 2013 at 1:57 PM, 林行众 <linxzh1989 at gmail.com> wrote:
>> I want to install biopython 1.61 in a local server(CentOS),
>>     python setup.py build
>>     python setup.py test
>> and then showed some errors:
>>
>> ...
>>
>> i use python 2.6.5
>>
>
> Thank you for getting in touch, and including the important
> information about the operating system, version of Python
> and version of Biopython.
>
>> FAIL: Test an input file containing a single sequence.
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "test_Clustalw_tool.py", line 166, in test_single_sequence
>>     self.assertTrue(str(err) == "No records found in handle")
>> AssertionError
>>
>
> This test calls the command line tool clustalw.
>
> What version of clustalw do you have?
>
>> ERROR: Test Entrez.read from URL
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "test_Entrez_online.py", line 34, in test_read_from_url
>>     rec = Entrez.read(einfo)
>>   File
"/share/fg2/Linxzh/biopython-1.61/build/lib.linux-x86_64-2.6/Bio/Entrez/__init__.py",
>> line 362, in read
>>     record = handler.read(handle)
>>   File
"/share/fg2/Linxzh/biopython-1.61/build/lib.linux-x86_64-2.6/Bio/Entrez/Parser.py",
>> line 184, in read
>>     self.parser.ParseFile(handle)
>>   File
"/share/fg2/Linxzh/biopython-1.61/build/lib.linux-x86_64-2.6/Bio/Entrez/Parser.py",
>> line 322, in endElementHandler
>>     raise RuntimeError(value)
>> RuntimeError: Unable to open connection to #DbInfo?dbaf=
>>
>
> This test connects to the NCBI Entrez server over the internet.
> This kind of error is usually a temporary network problem, and
> will go away if you repeat the test later.
>
>> ERROR: Run tutorial doctests.
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "test_Tutorial.py", line 152, in test_doctests
>> ValueError: 4 Tutorial doctests failed: test_from_line_05671,
>> test_from_line_06030, test_from_line_06190, test_from_line_06479
>
> Those four failing examples in the Tutorial seem to match this
> commit, made just before the Biopython 1.61 release:
>
> https://github.com/biopython/biopython/commit/b84bda01bd22e93a1cf71613a55
February 2013 (Biopython
1.61)cfca876b7128d7#Doc/Tutorial.tex<https://github.com/biopython/biopython/commit/b84bda01bd22e93a1cf71613a5cfca876b7128d7#Doc/Tutorial.tex>
>
> Where did you get the Biopython 1.61 files from? e.g. The zip file
> or tar.gz file on our website? Perhaps I accidentally included an
> older copy of the Doc/Tutorial.tex file? Could you look for the
> "Late Update" line in your Tutorial.tex file for me - does it say:
>
> \date{Last Update -- 5 February 2013 (Biopython 1.61)}
>
> Thanks,
>
> Peter

Hi，Peter！
Clustalw I am using is 1.83.

I've found the 'Late Update' in Tutorial.tex, it's ' \date{Last Update -- 5
February 2013 (Biopython 1.61)}'.

I downloaded the tar.gz from the biopython website.

Thanks
Lin