[Debian-med-packaging] Bug#1027335: Bug#1027335: pairtools -- FTBFS in unstable

[Étienne Mollier]

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 <emollier at 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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