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Dear Iddo,<br>
<br>
After reading here: <br>
<br>
<a class="moz-txt-link-freetext" href="https://docs.python.org/3/install/">https://docs.python.org/3/install/</a><br>
<br>
I would assume that your built Biopython stuff is in a "build"
subfolder (including the C extensions), but you are running the
test from the source folder (biopython-master). Could this be?<br>
<br>
Best<br>
Markus<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">Am 20.10.2022 um 08:41 schrieb Markus
Piotrowski:<br>
</div>
<blockquote type="cite"
cite="mid:6c9d3e8f-10b0-e8f9-4bba-331c0cf0eb53@ruhr-uni-bochum.de">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
This may be a naive question, since I'm not very familiar with
installing from source, but does "build" compile the C extensions
or is this something that happens during "install"? In the first
case you would be missing the compiled C-extension, leading to the
described import error.<br>
<br>
Best<br>
Markus<br>
<br>
<div class="moz-cite-prefix">Am 20.10.2022 um 01:58 schrieb Iddo
Friedberg:<br>
</div>
<blockquote type="cite"
cite="mid:CABm4-MQrw-fpXLJN+qGYckN=dLJTa_LXWvO4PAYaMxYC6oJweg@mail.gmail.com">
<meta http-equiv="content-type" content="text/html;
charset=UTF-8">
<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
(this seems to be concluding fine)
python setup.py test
And the first error line (of many) is:
/home/idoerg/Downloads/biopython-master/Bio/__init__.py:138: 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/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" moz-do-not-send="true"
class="moz-txt-link-freetext">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 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>
</div>
<div
id="m_5327145556957949328m_666267887992158593yahoo_quoted_7204585151">
<div style="font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px;color:rgb(38,40,42)">
<div> On Thursday, October 20, 2022 at 01:43:28 AM
GMT+9, Iddo Friedberg <<a
href="mailto:idoerg@gmail.com" rel="noreferrer"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">idoerg@gmail.com</a>>
wrote: </div>
<div><br>
</div>
<div><br>
</div>
<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" moz-do-not-send="true"
class="moz-txt-link-freetext">http://iddo-friedberg.net/contact.html</a><br>
++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.><br>
++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.<br>
.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>><br>
>>----.<--.>++++++.<<<<------------------------------------.<br>
</div>
</div>
</div>
</div>
</div>
_______________________________________________<br>
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<br>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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<br>
<pre class="moz-signature" cols="72">--
_________________________________
Dr. Markus Piotrowski
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<br>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
_________________________________
Dr. Markus Piotrowski
Privatdozent/Akademischer Rat
Lehrstuhl für Molekulargenetik und Physiologie der Pflanzen
ND 3/49
Universitätsstr. 150
44801 Bochum
Tel. xx49-(0)234-3224290
Fax. xx49-(0)234-3214187
<a class="moz-txt-link-freetext" href="https://www.ruhr-uni-bochum.de/pflaphy/Seiten_dt/Piotrowski_d.html">https://www.ruhr-uni-bochum.de/pflaphy/Seiten_dt/Piotrowski_d.html</a>
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