[Biopython] problem with Bio.Align _aligns.c

Wed Jun 27 03:11:05 UTC 2018

 Francesco, in which directory are you running Python?I can replicate this error only if I try these commands in the biopython source directory. In that case, python imports from the current directory, not from the installed directory.Importing Bio.Cluster will also fail for the same reason.Numpy has the same problem; there they show an informative error message if somebody tries to import numpy from the source tree:
>>> from numpy import *
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "numpy/__init__.py", line 131, in <module>
    raise ImportError(msg)
ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.

-Michiel

    On Wednesday, June 27, 2018, 6:38:02 AM GMT+9, Fulton, Ben <befulton at iu.edu> wrote:  

 #yiv8000510501 #yiv8000510501 -- _filtered #yiv8000510501 {panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv8000510501 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;}#yiv8000510501 #yiv8000510501 p.yiv8000510501MsoNormal, #yiv8000510501 li.yiv8000510501MsoNormal, #yiv8000510501 div.yiv8000510501MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv8000510501 a:link, #yiv8000510501 span.yiv8000510501MsoHyperlink {color:blue;text-decoration:underline;}#yiv8000510501 a:visited, #yiv8000510501 span.yiv8000510501MsoHyperlinkFollowed {color:purple;text-decoration:underline;}#yiv8000510501 p.yiv8000510501msonormal0, #yiv8000510501 li.yiv8000510501msonormal0, #yiv8000510501 div.yiv8000510501msonormal0 {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv8000510501 span.yiv8000510501EmailStyle20 {font-family:sans-serif;color:windowtext;}#yiv8000510501 .yiv8000510501MsoChpDefault {font-size:10.0pt;} _filtered #yiv8000510501 {margin:1.0in 1.0in 1.0in 1.0in;}#yiv8000510501 div.yiv8000510501WordSection1 {}#yiv8000510501 
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: 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>
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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