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<div>Francesco, in which directory are you running Python?</div><div>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.</div><div>Importing Bio.Cluster will also fail for the same reason.</div><div>Numpy has the same problem; there they show an informative error message if somebody tries to import numpy from the source tree:</div><div><br></div><div><span>>>> from numpy import *<br>Traceback (most recent call last):<br> File "<stdin>", line 1, in <module><br> File "numpy/__init__.py", line 131, in <module><br> raise ImportError(msg)<br>ImportError: Error importing numpy: you should not try to import numpy from<br> its source directory; please exit the numpy source tree, and relaunch<br> your python interpreter from there.<br></span><span></span><div><br></div><div><br></div><div>-Michiel<br></div></div><div><br></div>
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On Wednesday, June 27, 2018, 6:38:02 AM GMT+9, Fulton, Ben <befulton@iu.edu> wrote:
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#yiv8000510501 </style><div><div class="yiv8000510501WordSection1"><p class="yiv8000510501MsoNormal">Wouldn’t you have to run “python setup.py install” to get the libraries into the correct locations?</p><p class="yiv8000510501MsoNormal"> </p><div><p class="yiv8000510501MsoNormal"><span style="color:#1F497D;">--</span></p><p class="yiv8000510501MsoNormal"><span style="color:#1F497D;">Ben Fulton</span></p><p class="yiv8000510501MsoNormal"><span style="color:#1F497D;">Research Technologies</span></p><p class="yiv8000510501MsoNormal"><span style="color:#1F497D;">Scientific Applications and Performance Tuning</span></p><p class="yiv8000510501MsoNormal"><span style="color:#1F497D;">Indiana University</span></p><p class="yiv8000510501MsoNormal"><span style="color:#1F497D;">E-Mail: </span><a rel="nofollow" shape="rect" ymailto="mailto:befulton@iu.edu" target="_blank" href="mailto:befulton@iu.edu"><span style="color:#0563C1;">befulton@iu.edu</span></a><span style="color:#1F497D;"></span></p></div><p class="yiv8000510501MsoNormal"> </p><div class="yiv8000510501yqt2137137129" id="yiv8000510501yqt84426"><div><div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in;"><p class="yiv8000510501MsoNormal"><b>From:</b> Biopython <biopython-bounces+befulton=iu.edu@mailman.open-bio.org> <b>On Behalf Of </b>Francesco Gastaldello (Staff)<br clear="none"><b>Sent:</b> Tuesday, June 26, 2018 10:36 AM<br clear="none"><b>To:</b> p.j.a.cock@googlemail.com<br clear="none"><b>Cc:</b> biopython@mailman.open-bio.org<br clear="none"><b>Subject:</b> Re: [Biopython] problem with Bio.Align _aligns.c</p></div></div><p class="yiv8000510501MsoNormal"> </p><div id="yiv8000510501divtagdefaultwrapper"><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.</span></p><p><span style="font-size:12.0pt;color:black;"> </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 clear="none"><br clear="none">I've run some tests even on the master branch, which I consider to be stable environment.</span></p><p><span style="font-size:12.0pt;color:black;"> </span></p><p><span style="font-size:12.0pt;color:black;">Francesco </span></p></div><div class="yiv8000510501MsoNormal" style="text-align:center;" align="center"><hr width="98%" size="3" align="center"></div><div id="yiv8000510501divRplyFwdMsg"><p class="yiv8000510501MsoNormal"><b><span style="color:black;">From:</span></b><span style="color:black;"> Peter Cock <<a rel="nofollow" shape="rect" ymailto="mailto:p.j.a.cock@googlemail.com" target="_blank" href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>><br clear="none"><b>Sent:</b> 26 June 2018 15:29:39<br clear="none"><b>To:</b> Francesco Gastaldello (Staff)<br clear="none"><b>Cc:</b> <a rel="nofollow" shape="rect" ymailto="mailto:biopython@mailman.open-bio.org" target="_blank" href="mailto:biopython@mailman.open-bio.org">biopython@mailman.open-bio.org</a><br clear="none"><b>Subject:</b> Re: [Biopython] problem with Bio.Align _aligns.c</span> </p><div><p class="yiv8000510501MsoNormal"> </p></div></div><div><div><p class="yiv8000510501MsoNormal">You must be running from Git, perhaps even the<br clear="none">provisional tag for Biopython 1.72?<br clear="none"><br clear="none">The error is worryingly similar to what I am getting<br clear="none">with the automated wheels for Linux and macOS<br clear="none">under TravisCI - they seem to build fine, but when<br clear="none">running the tests, the compiled code can't be found.<br clear="none"><br clear="none">This is holding up the Biopython 1.72 release, see also:<br clear="none"><a rel="nofollow" shape="rect" target="_blank" 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 clear="none"><br clear="none">Do you see this with other C code as well, e.g.<br clear="none">Bio.Cluster, or cpairwise2, or KDTree?<br clear="none"><br clear="none">Perhaps this is a problem with the current code in<br clear="none">GitHub, not just something strange with the multi-<br clear="none">wheel setup as I had been assuming?<br clear="none"><br clear="none">Peter<br clear="none"><br clear="none">On Tue, Jun 26, 2018 at 12:26 PM, Francesco Gastaldello (Staff)<br clear="none"><<a rel="nofollow" shape="rect" ymailto="mailto:f.gastaldello@dundee.ac.uk" target="_blank" href="mailto:f.gastaldello@dundee.ac.uk">f.gastaldello@dundee.ac.uk</a>> wrote:<br clear="none">> Hi all,<br clear="none">><br clear="none">><br clear="none">> I have a virtual environment with python 2.7.15rc1 and I get this error when<br clear="none">> I run some commands:<br clear="none">><br clear="none">><br clear="none">> ////<br clear="none">><br clear="none">> Python 2.7.15rc1 (default, Apr 15 2018, 21:51:34)<br clear="none">> [GCC 7.3.0] on linux2<br clear="none">> Type "help", "copyright", "credits" or "license" for more information.<br clear="none">>>>> from Bio import SeqIO<br clear="none">> Traceback (most recent call last):<br clear="none">> File "<stdin>", line 1, in <module><br clear="none">> File "Bio/SeqIO/__init__.py", line 375, in <module><br clear="none">> from Bio.Align import MultipleSeqAlignment<br clear="none">> File "Bio/Align/__init__.py", line 22, in <module><br clear="none">> from Bio.Align import _aligners<br clear="none">> ImportError: cannot import name _aligners<br clear="none">><br clear="none">> ////<br clear="none">><br clear="none">><br clear="none">> I've made sure to run "python setup.py build" before trying anything but<br clear="none">> that did not solve the problem.<br clear="none">><br clear="none">> I'm on Ububtu 18.04 on a virtual machine.<br clear="none">><br clear="none">><br clear="none">> Thanks,<br clear="none">><br clear="none">> Francesco<br clear="none">><br clear="none">><br clear="none">> The University of Dundee is a registered Scottish Charity, No: SC015096<br clear="none">><br clear="none">> _______________________________________________<br clear="none">> Biopython mailing list - <a rel="nofollow" shape="rect" ymailto="mailto:Biopython@mailman.open-bio.org" target="_blank" href="mailto:Biopython@mailman.open-bio.org">Biopython@mailman.open-bio.org</a><br clear="none">> <a rel="nofollow" shape="rect" target="_blank" href="http://mailman.open-bio.org/mailman/listinfo/biopython">http://mailman.open-bio.org/mailman/listinfo/biopython</a></p></div></div><p class="yiv8000510501MsoNormal"><br clear="none"><span style="font-size:10.0pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span> </p></div></div></div></div><div class="yqt2137137129" id="yqt90376">_______________________________________________<br clear="none">Biopython mailing list - <a shape="rect" ymailto="mailto:Biopython@mailman.open-bio.org" href="mailto:Biopython@mailman.open-bio.org">Biopython@mailman.open-bio.org</a><br clear="none"><a shape="rect" href="http://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython</a></div></div>
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