[Biopython] install from source: is this an issue?

Markus Piotrowski Markus.Piotrowski at ruhr-uni-bochum.de
Thu Oct 20 03:16:38 EDT 2022


Dear Iddo,

After reading here:

https://docs.python.org/3/install/

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?

Best
Markus



Am 20.10.2022 um 08:41 schrieb Markus Piotrowski:
> 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.
>
> Best
> Markus
>
> Am 20.10.2022 um 01:58 schrieb Iddo Friedberg:
>> Hi,
>>
>> Thank you for your answer, Michiel.
>>
>> So I'm confused as to what I am doing wrong. I downloaded the zip , 
>> unzipped, changed to the biopython-master directory, and ran
>> 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
>> Thanks,
>>
>> Iddo
>>
>> --
>> Sent from a machine that promotes typos
>>
>> On Wed, Oct 19, 2022, 17:15 Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>>
>>     Hi Iddo,
>>
>>
>>     > The first error "BiopythonWarning: You may be importing
>>     Biopython from inside the source tree."
>>     > Is that something I can ignore,
>>
>>     No; it is causing the import error.
>>
>>     Best,
>>     -Michiel
>>
>>     On Thursday, October 20, 2022 at 01:43:28 AM GMT+9, Iddo
>>     Friedberg <idoerg at gmail.com> wrote:
>>
>>
>>     Hi,
>>
>>     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.
>>
>>     However, I am encountering the following problem when trying to test:
>>
>>
>>     idoerg at IddoWS:~/soft/biopython$ python setup.py test
>>     running test
>>     Python version: 3.7.5 (default, Dec  9 2021, 17:04:37)
>>     [GCC 8.4.0]
>>     Operating system: posix linux
>>     /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
>>       BiopythonWarning,
>>     test_Ace ... ok
>>     test_Affy ... ok
>>     test_AlignIO ... loading tests failed:
>>     Failed to import test module: test_AlignIO
>>     Traceback (most recent call last):
>>       File "/usr/lib/python3.7/unittest/loader.py", line 154, in
>>     loadTestsFromName
>>         module = __import__(module_name)
>>       File "/home/idoerg/soft/biopython/Tests/test_AlignIO.py", line
>>     11, in <module>
>>         from Bio import AlignIO
>>       File "/home/idoerg/soft/biopython/Bio/AlignIO/__init__.py",
>>     line 140, in <module>
>>         from Bio.Align import MultipleSeqAlignment
>>       File "/home/idoerg/soft/biopython/Bio/Align/__init__.py", line
>>     34, in <module>
>>         from Bio.Align import _aligners
>>     ImportError: cannot import name '_aligners' from 'Bio.Align'
>>     (/home/idoerg/soft/biopython/Bio/Align/__init__.py)
>>
>>     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 "BiopythonWarning: You may be
>>     importing Biopython from inside the source tree."
>>
>>     Is that something I can ignore, or am I doing yet another thing
>>     wrong?
>>
>>     Thanks,
>>
>>     Iddo
>>
>>     -- 
>>     Iddo Friedberg
>>     http://iddo-friedberg.net/contact.html
>>     ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
>>     ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
>>     .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>     >>----.<--.>++++++.<<<<------------------------------------.
>>     _______________________________________________
>>     Biopython mailing list  - Biopython at biopython.org
>>     https://mailman.open-bio.org/mailman/listinfo/biopython
>>
>>
>> _______________________________________________
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>
> -- 
> _________________________________
> Dr. Markus Piotrowski
> Privatdozent/Akademischer Rat
> Lehrstuhl für Molekulargenetik und Physiologie der Pflanzen
> ND 3/49
> Universitätsstr. 150
> 44801 Bochum
>
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-- 
_________________________________
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

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