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<p style="margin-top:0;margin-bottom:0">I'm running the test via Pycharm and it is connected to my origin and upstream branches on GitHub.</p>
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<p style="margin-top:0;margin-bottom:0">I've done a quick test of the other modules that use C and I can confirm that the same problem is visible.<br>
<br>
I've run some tests even on the master branch, which I consider to be stable environment.</p>
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<p style="margin-top:0;margin-bottom:0">Francesco </p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Peter Cock <p.j.a.cock@googlemail.com><br>
<b>Sent:</b> 26 June 2018 15:29:39<br>
<b>To:</b> Francesco Gastaldello (Staff)<br>
<b>Cc:</b> biopython@mailman.open-bio.org<br>
<b>Subject:</b> Re: [Biopython] problem with Bio.Align _aligns.c</font>
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<div class="PlainText">You must be running from Git, perhaps even the<br>
provisional tag for Biopython 1.72?<br>
<br>
The error is worryingly similar to what I am getting<br>
with the automated wheels for Linux and macOS<br>
under TravisCI - they seem to build fine, but when<br>
running the tests, the compiled code can't be found.<br>
<br>
This is holding up the Biopython 1.72 release, see also:<br>
<a href="http://mailman.open-bio.org/pipermail/biopython/2018-June/016474.html">http://mailman.open-bio.org/pipermail/biopython/2018-June/016474.html</a><br>
<br>
Do you see this with other C code as well, e.g.<br>
Bio.Cluster, or cpairwise2, or KDTree?<br>
<br>
Perhaps this is a problem with the current code in<br>
GitHub, not just something strange with the multi-<br>
wheel setup as I had been assuming?<br>
<br>
Peter<br>
<br>
On Tue, Jun 26, 2018 at 12:26 PM, Francesco Gastaldello (Staff)<br>
<f.gastaldello@dundee.ac.uk> wrote:<br>
> Hi all,<br>
><br>
><br>
> I have a virtual environment with python 2.7.15rc1 and I get this error when<br>
> I run some commands:<br>
><br>
><br>
> ////<br>
><br>
> Python 2.7.15rc1 (default, Apr 15 2018, 21:51:34)<br>
> [GCC 7.3.0] on linux2<br>
> Type "help", "copyright", "credits" or "license" for more information.<br>
>>>> from Bio import SeqIO<br>
> Traceback (most recent call last):<br>
> File "<stdin>", line 1, in <module><br>
> File "Bio/SeqIO/__init__.py", line 375, in <module><br>
> from Bio.Align import MultipleSeqAlignment<br>
> File "Bio/Align/__init__.py", line 22, in <module><br>
> from Bio.Align import _aligners<br>
> ImportError: cannot import name _aligners<br>
><br>
> ////<br>
><br>
><br>
> I've made sure to run "python setup.py build" before trying anything but<br>
> that did not solve the problem.<br>
><br>
> I'm on Ububtu 18.04 on a virtual machine.<br>
><br>
><br>
> Thanks,<br>
><br>
> Francesco<br>
><br>
><br>
> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
><br>
> _______________________________________________<br>
> Biopython mailing list - Biopython@mailman.open-bio.org<br>
> <a href="http://mailman.open-bio.org/mailman/listinfo/biopython">http://mailman.open-bio.org/mailman/listinfo/biopython</a><br>
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</span></font></div>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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