<div dir="ltr"><div dir="auto">Hi,<div dir="auto"><br></div><div>Thank you for your answer, Michiel.</div><div><br></div><div dir="auto">So I'm confused as to what I am doing wrong. I downloaded the zip , unzipped, changed to the biopython-master directory, and ran <br></div><div dir="auto"><pre>python setup.py build<br>(this seems to be concluding fine)<br>
python setup.py test<br><br>And the first error line (of many) is:<br>/home/idoerg/Downloads/biopython-master/Bio/__init__.py:138: BiopythonWarning: You may be importing Biopython from inside the source tree. <br>This is bad practice and might lead to downstream issues. In particular, you might encounter ImportErrors due to missing compiled C extensions.<br>We recommend that you try running your code from outside the source tree. <br>If you are outside the source tree then you have a setup.py file in an unexpected directory: /home/idoerg/Downloads/biopython-master</pre></div><div>Thanks,</div><div><br></div><div>Iddo</div><div><br></div><div dir="auto"><div data-smartmail="gmail_signature" dir="auto">--<br>Sent from a machine that promotes typos</div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Oct 19, 2022, 17:15 Michiel de Hoon <<a href="mailto:mjldehoon@yahoo.com" target="_blank">mjldehoon@yahoo.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div style="font-family:Helvetica Neue,Helvetica,Arial,sans-serif;font-size:10px"><div></div>
<div dir="ltr">Hi Iddo,</div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">> The first error "<span style="font-family:monospace">BiopythonWarning: You may be importing Biopython from inside the source tree."<span style="font-family:arial,sans-serif"> </span></span><br><span style="font-family:monospace"><span style="font-family:arial,sans-serif"></span></span><div><span style="font-family:monospace"><span style="font-family:arial,sans-serif">> Is that something I can ignore, <br></span></span></div><div><span style="font-family:monospace"><span style="font-family:arial,sans-serif"><br></span></span></div><div dir="ltr"><span style="font-family:monospace"><span style="font-family:arial,sans-serif">No; it is causing the import error.</span></span></div><div dir="ltr"><span style="font-family:monospace"><span style="font-family:arial,sans-serif"><br></span></span></div><div dir="ltr"><span style="font-family:monospace"><span style="font-family:arial,sans-serif">Best,</span></span></div><div dir="ltr"><span style="font-family:monospace"><span style="font-family:arial,sans-serif">-Michiel<br></span></span></div><div><br></div></div>
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On Thursday, October 20, 2022 at 01:43:28 AM GMT+9, Iddo Friedberg <<a href="mailto:idoerg@gmail.com" rel="noreferrer" target="_blank">idoerg@gmail.com</a>> wrote:
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<div><div id="m_5327145556957949328m_666267887992158593yiv3039875215"><div dir="ltr"><div>Hi,</div><div><br></div><div>I'm trying to install biopython from source, since release 1.79 does not work with the newest Swissprot FT records. Looking at the source of SwissProt/__init__.py in github this issue seems to be fixed and hopefully release 1.80 this will work again. <br><br></div><div>However, I am encountering the following problem when trying to test:<br></div><div><br></div><div><br></div><span style="font-family:monospace">idoerg@IddoWS:~/soft/biopython$ python setup.py test<br>running test<br>Python version: 3.7.5 (default, Dec 9 2021, 17:04:37) <br>[GCC 8.4.0]<br>Operating system: posix linux<br>/home/idoerg/soft/biopython/Bio/__init__.py:146: BiopythonWarning: You may be importing Biopython from inside the source tree. This is bad practice and might lead to downstream issues. In particular, you might encounter ImportErrors due to missing compiled C extensions. We recommend that you try running your code from outside the source tree. If you are outside the source tree then you have a setup.py file in an unexpected directory: /home/idoerg/soft/biopython<br> BiopythonWarning,<br>test_Ace ... ok<br>test_Affy ... ok<br>test_AlignIO ... loading tests failed:<br>Failed to import test module: test_AlignIO<br>Traceback (most recent call last):<br> File "/usr/lib/python3.7/unittest/loader.py", line 154, in loadTestsFromName<br> module = __import__(module_name)<br> File "/home/idoerg/soft/biopython/Tests/test_AlignIO.py", line 11, in <module><br> from Bio import AlignIO<br> File "/home/idoerg/soft/biopython/Bio/AlignIO/__init__.py", line 140, in <module><br> from Bio.Align import MultipleSeqAlignment<br> File "/home/idoerg/soft/biopython/Bio/Align/__init__.py", line 34, in <module><br> from Bio.Align import _aligners<br>ImportError: cannot import name '_aligners' from 'Bio.Align' (/home/idoerg/soft/biopython/Bio/Align/__init__.py)</span><br><div><br></div><div>Previous iterations of the "_aligners" import error error in the biopython github were attributed to conflicting python versions. This may be the case here, but before I kill all my anaconda stuff, I just wanted to make sure that I'm actually running the test correctly. The first error "<span style="font-family:monospace">BiopythonWarning: You may be importing Biopython from inside the source tree."<span style="font-family:arial,sans-serif"> <br></span></span></div><div><span style="font-family:monospace"><span style="font-family:arial,sans-serif"><br></span></span></div><div><span style="font-family:monospace"><span style="font-family:arial,sans-serif">Is that something I can ignore, or am I doing yet another thing wrong?</span></span></div><div><span style="font-family:monospace"><br></span></div><div><span style="font-family:monospace">Thanks,</span></div><div><span style="font-family:monospace"><br></span></div><div><span style="font-family:monospace">Iddo<br></span> </div><br>-- <br><div dir="ltr"><div dir="ltr"><div>Iddo Friedberg</div><div><a rel="nofollow noopener noreferrer noreferrer" href="http://iddo-friedberg.net/contact.html" target="_blank">http://iddo-friedberg.net/contact.html</a><br>++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.><br>++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.<br>.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>><br>>>----.<--.>++++++.<<<<------------------------------------.<br></div></div></div></div>
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