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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Wouldn’t you have to run “python setup.py install” to get the libraries into the correct locations?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><span style='color:#1F497D'>--<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Ben Fulton<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Research Technologies<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Scientific Applications and Performance Tuning<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Indiana University<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>E-Mail: </span><a href="mailto:befulton@iu.edu"><span style='color:#0563C1'>befulton@iu.edu</span></a><span style='color:#1F497D'><o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b>From:</b> Biopython <biopython-bounces+befulton=iu.edu@mailman.open-bio.org> <b>On Behalf Of </b>Francesco Gastaldello (Staff)<br><b>Sent:</b> Tuesday, June 26, 2018 10:36 AM<br><b>To:</b> p.j.a.cock@googlemail.com<br><b>Cc:</b> biopython@mailman.open-bio.org<br><b>Subject:</b> Re: [Biopython] problem with Bio.Align _aligns.c<o:p></o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div id=divtagdefaultwrapper><p><span style='font-size:12.0pt;color:black'>I'm running the test via Pycharm and it is connected to my origin and upstream branches on GitHub.<o:p></o:p></span></p><p><span style='font-size:12.0pt;color:black'><o:p> </o:p></span></p><p><span style='font-size:12.0pt;color:black'>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.<o:p></o:p></span></p><p><span style='font-size:12.0pt;color:black'><o:p> </o:p></span></p><p><span style='font-size:12.0pt;color:black'>Francesco <o:p></o:p></span></p></div><div class=MsoNormal align=center style='text-align:center'><hr size=3 width="98%" align=center></div><div id=divRplyFwdMsg><p class=MsoNormal><b><span style='color:black'>From:</span></b><span style='color:black'> Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>><br><b>Sent:</b> 26 June 2018 15:29:39<br><b>To:</b> Francesco Gastaldello (Staff)<br><b>Cc:</b> <a href="mailto:biopython@mailman.open-bio.org">biopython@mailman.open-bio.org</a><br><b>Subject:</b> Re: [Biopython] problem with Bio.Align _aligns.c</span> <o:p></o:p></p><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>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><<a href="mailto:f.gastaldello@dundee.ac.uk">f.gastaldello@dundee.ac.uk</a>> 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 - <a href="mailto:Biopython@mailman.open-bio.org">Biopython@mailman.open-bio.org</a><br>> <a href="http://mailman.open-bio.org/mailman/listinfo/biopython">http://mailman.open-bio.org/mailman/listinfo/biopython</a><o:p></o:p></p></div></div><p class=MsoNormal><br><span style='font-size:10.0pt'>The University of Dundee is a registered Scottish Charity, No: SC015096</span> <o:p></o:p></p></div></body></html>