Re: [Biopython] install from source: is this an issue?
Markus Piotrowski <[email protected]> Thu, 20 Oct 2022 09:16:38 +0200
| Newsgroups | gmane.comp.python.bio.general |
|---|---|
| Message-ID | <[email protected]> |
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 <[email protected]> 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 <[email protected]> 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@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 - [email protected] >> https://mailman.open-bio.org/mailman/listinfo/biopython >> >> >> _______________________________________________ >> Biopython mailing list [email protected] >> https://mailman.open-bio.org/mailman/listinfo/biopython > > -- > _________________________________ > 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 > > _______________________________________________ > Biopython mailing list [email protected] > https://mailman.open-bio.org/mailman/listinfo/biopython -- _________________________________ 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 _______________________________________________ Biopython mailing list - [email protected] https://mailman.open-bio.org/mailman/listinfo/biopython