[Biopython] problem with Bio.Align _aligns.c

[Francesco Gastaldello (Staff)]

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>
Sent: 26 June 2018 15:29:39
To: Francesco Gastaldello (Staff)
Cc: 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> 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
>
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