Control: tags -1 + confirmed Control: reassign -1 src:python-pysam 0.20.0+ds-2 Control: affects -1 src:pairtools
Hi Nilesh,
Nilesh Patra, on 2022-12-30:
> File "/<<PKGBUILDDIR>>/setup.py", line 130, in <module>
> ext_modules=get_ext_modules(),
> ^^^^^^^^^^^^^^^^^
> File "/<<PKGBUILDDIR>>/setup.py", line 81, in get_ext_modules
> extra_link_args=pysam.get_libraries(),
> ^^^^^^^^^^^^^^^^^^^^^
> File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 100, in
> get_libraries
> return [os.path.join(dirname, x + so) for x in pysam_libs]
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 100, in
> <listcomp>
> return [os.path.join(dirname, x + so) for x in pysam_libs]
> ~~^~~~
> TypeError: can only concatenate str (not "NoneType") to str
Thanks for catching this, I confirm I can reproduce the error
without pairtools in the loop. Given the reproducer.py below:
import pysam
for lib in pysam.get_libraries():
print(lib)
I do get the error with python3.11:
$ python3.11 reproducer.py
Traceback (most recent call last):
File "/home/emollier/tmp/reproducer.py", line 2, in <module>
for lib in pysam.get_libraries():
^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 100, in
get_libraries
return [os.path.join(dirname, x + so) for x in pysam_libs]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 100, in
<listcomp>
return [os.path.join(dirname, x + so) for x in pysam_libs]
~~^~~~
TypeError: can only concatenate str (not "NoneType") to str
Besides, the error looks genuine since in python3.10, the output
seems to return the expected result:
$ python3.10 reproducer.py
/usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-310-x86_64-linux-gnu.so
/usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-310-x86_64-linux-gnu.so
/usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-310-x86_64-linux-gnu.so
/usr/lib/python3/dist-packages/pysam/libcvcf.cpython-310-x86_64-linux-gnu.so
/usr/lib/python3/dist-packages/pysam/libcbcf.cpython-310-x86_64-linux-gnu.so
/usr/lib/python3/dist-packages/pysam/libctabix.cpython-310-x86_64-linux-gnu.so
So I'm reassigning the issue accordingly.
Have a nice day, :)
--
Étienne Mollier <emoll...@emlwks999.eu>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/1, please excuse my verbosity.
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