[Biopython] Problem installing biopython with Python 3.3.1.rc1

[Nicolas Joannin]

Hi Peter,

Thanks for the quick reply!
Indeed, I don't think it is a big issue for me, and I have also not had any
problems with Python 3.3.0 on another machine.
So, yes, it probably is linked to the Python 3.3.1rc1...

However, I should point out that it is not only the Bio.bgzf that fails
testing.
There are also test_Entrez_online and test_SeqIO_index that are indicated
as "FAIL" (both of which I do not directly use).

Cheers,
Nicolas



Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



On Sun, Apr 7, 2013 at 3:19 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Sat, Apr 6, 2013 at 4:31 PM, Nicolas Joannin
> <nicolas.joannin at gmail.com> wrote:
> > Hello everyone,
> >
> > I'm having a problem installing biopython with Python 3.3.1rc1...
> > Basically, I get several tests failing (in addition to a lot of
> warnings).
> >
> > I don't think the failed tests will be a problem for my work, however, I
> > thought you'd want to have a look... Attached is the output of python3
> > setup.py test.
> >
> > Also, if you think I shouldn't use biopython without having these failed
> > tests fixed first, please let me know!
> >
> > Best regards,
> > Nicolas
>
> Hi Nicolas,
>
> You should be OK installing this - all the test failures are
> within Bio.bgzf which is curious, but you probably won't be
> using BGZF compressed files.
>
> We do have buildslaves testing on Python 3.3.0 where this
> does not happen, so perhaps this is a new failure from a
> change in Python 3.3.1rc1 - hopefully I'll be able to confirm
> that by updating one of the buildslaves.
>
> Thanks for the alert,
>
> Peter
>