[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
>> ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
>> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
>> .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>> >>----.<--.>++++++.<<<<------------------------------------.
>> _______________________________________________
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>>
>>
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>
> --
> _________________________________
> Dr. Markus Piotrowski
> Privatdozent/Akademischer Rat
> Lehrstuhl für Molekulargenetik und Physiologie der Pflanzen
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> Universitätsstr. 150
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>
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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
https://www.ruhr-uni-bochum.de/pflaphy/Seiten_dt/Piotrowski_d.html
http://homepage.ruhr-uni-bochum.de/Markus.Piotrowski/Index.html
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