[Biopython] problem with Bio.Align _aligns.c

[Fulton, Ben]

Wouldn't you have to run "python setup.py install" to get the libraries into
the correct locations?

 

--

Ben Fulton

Research Technologies

Scientific Applications and Performance Tuning

Indiana University

E-Mail:  <mailto:befulton at iu.edu> befulton at iu.edu

 

From: Biopython <biopython-bounces+befulton=iu.edu at mailman.open-bio.org> On
Behalf Of Francesco Gastaldello (Staff)
Sent: Tuesday, June 26, 2018 10:36 AM
To: p.j.a.cock at googlemail.com
Cc: biopython at mailman.open-bio.org
Subject: Re: [Biopython] problem with Bio.Align _aligns.c

 

I'm running the test via Pycharm and it is connected to my origin and
upstream branches on GitHub.

 

I've done a quick test of the other modules that use C and I can confirm
that the same problem is visible.

I've run some tests even on the master branch, which I consider to be stable
environment.

 

Francesco 

  _____  

From: Peter Cock <p.j.a.cock at googlemail.com
<mailto:p.j.a.cock at googlemail.com> >
Sent: 26 June 2018 15:29:39
To: Francesco Gastaldello (Staff)
Cc: biopython at mailman.open-bio.org <mailto:biopython at mailman.open-bio.org> 
Subject: Re: [Biopython] problem with Bio.Align _aligns.c 

 

You must be running from Git, perhaps even the
provisional tag for Biopython 1.72?

The error is worryingly similar to what I am getting
with the automated wheels for Linux and macOS
under TravisCI - they seem to build fine, but when
running the tests, the compiled code can't be found.

This is holding up the Biopython 1.72 release, see also:
http://mailman.open-bio.org/pipermail/biopython/2018-June/016474.html

Do you see this with other C code as well, e.g.
Bio.Cluster, or cpairwise2, or KDTree?

Perhaps this is a problem with the current code in
GitHub, not just something strange with the multi-
wheel setup as I had been assuming?

Peter

On Tue, Jun 26, 2018 at 12:26 PM, Francesco Gastaldello (Staff)
<f.gastaldello at dundee.ac.uk <mailto:f.gastaldello at dundee.ac.uk> > wrote:
> Hi all,
>
>
> I have a virtual environment with python 2.7.15rc1 and I get this error
when
> I run some commands:
>
>
> ////
>
> Python 2.7.15rc1 (default, Apr 15 2018, 21:51:34)
> [GCC 7.3.0] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from Bio import SeqIO
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "Bio/SeqIO/__init__.py", line 375, in <module>
>     from Bio.Align import MultipleSeqAlignment
>   File "Bio/Align/__init__.py", line 22, in <module>
>     from Bio.Align import _aligners
> ImportError: cannot import name _aligners
>
> ////
>
>
> I've made sure to run "python setup.py build" before trying anything but
> that did not solve the problem.
>
> I'm on Ububtu 18.04 on a virtual machine.
>
>
> Thanks,
>
> Francesco
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
<mailto:Biopython at mailman.open-bio.org> 
> http://mailman.open-bio.org/mailman/listinfo/biopython


The University of Dundee is a registered Scottish Charity, No: SC015096 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20180626/8be98d11/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 5687 bytes
Desc: not available
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20180626/8be98d11/attachment.p7s>