[Biopython-dev] Errors about installing biopython 1.61

[Peter Cock]

On Mon, May 13, 2013 at 2:41 AM, 林行众 <linxzh1989 at gmail.com> wrote:
>
>> 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.

Hi Lin,

I also have clustalw 1.83, so this isn't simply a version
problem. It could be something subtle about the locale -
what language is your CentOS running in (that can alter
error messages etc)?

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

That's good - that's what it should say :)

(Sorry late/last was my typing error).

>
> I downloaded the tar.gz from the biopython website.
>

Thanks. I could reproduce the test_Tutorial.py problem with that.
This is easy to explain - I forgot to include the test file my_blast.xml
when doing the release (and you are the first person to report this
problem). I should have noticed this myself, sorry :(

I've fixed this ready for the next release - thank you for reporting this:
https://github.com/biopython/biopython/commit/c1b63b88dd5a50fa3f6f2aef840a51fe9092e0c5

If you want to, you can get the missing file from here:
http://biopython.org/SRC/Doc/examples/my_blast.xml

or:
https://github.com/biopython/biopython/raw/master/Doc/examples/my_blast.xml

If you save that in the Biopython 1.61 source under Doc/examples
then the Tutorial test should pass.

--

Did you retry the test_Entrez_online.py example to see if
this was a temporary problem?

--

The good news is these minor issues should not cause you
any problems installing and using Biopython 1.61 - so you
can go ahead and run 'python setup.py install.

Thanks,

Peter