[Debian-med-packaging] Bug#1079439: Bug#1079439: python-biopython: autopkgtest stuck on riscv64

[Reinhard Tartler]

On 2024-08-23 15:59, Étienne Mollier wrote:
> Control: tags -1 + confirmed
> 
> Hi Reinhard,
> 
> Thanks for your time investigating this issue!  On the good news
> front, I confirm I can reproduce the problem with qemu-user, so
> this facilitate debugging even without direct access to the real
> hardware.
> [...]
> I'm at loss reasoning about the _makeResult method for now.
> Maybe there is something off about output handling by StringIO?
> I haven't dug further for the moment.

Actually, I've been able to compile pystack on the machine
(see https://github.com/bloomberg/pystack, and amazing tool)
and was able to get a trace of what the stuck process is doing:


Traceback for thread 3024343 (python3.12) [] (most recent call last):
     (Python) File 
"/home/siretart/python-biopython/.pybuild/cpython3_3.12/build/Tests/run_tests.py", 
line 343, in <module>
         errors = main(sys.argv[1:])
     (Python) File 
"/home/siretart/python-biopython/.pybuild/cpython3_3.12/build/Tests/run_tests.py", 
line 187, in main
         return runner.run()
     (Python) File 
"/home/siretart/python-biopython/.pybuild/cpython3_3.12/build/Tests/run_tests.py", 
line 324, in run
         ok = self.runTest(test)
     (Python) File 
"/home/siretart/python-biopython/.pybuild/cpython3_3.12/build/Tests/run_tests.py", 
line 281, in runTest
         suite.run(result)
     (Python) File "/usr/lib/python3.12/unittest/suite.py", line 122, in 
run
         test(result)
     (Python) File "/usr/lib/python3.12/unittest/suite.py", line 84, in 
__call__
         return self.run(*args, **kwds)
     (Python) File "/usr/lib/python3.12/unittest/suite.py", line 122, in 
run
         test(result)
     (Python) File "/usr/lib/python3.12/unittest/case.py", line 690, in 
__call__
         return self.run(*args, **kwds)
     (Python) File "/usr/lib/python3.12/unittest/case.py", line 634, in 
run
         self._callTestMethod(testMethod)
     (Python) File "/usr/lib/python3.12/unittest/case.py", line 589, in 
_callTestMethod
         if method() is not None:
     (Python) File 
"/home/siretart/python-biopython/.pybuild/cpython3_3.12/build/Tests/test_Align_codonalign.py", 
line 8242, in test_dn_ds
         dN, dS = calculate_dn_ds(pairwise_alignment, method="YN00")
     (Python) File 
"/home/siretart/python-biopython/.pybuild/cpython3_3.12/build/Bio/Align/analysis.py", 
line 88, in calculate_dn_ds
         return _yn00(codons1, codons2, codon_table)
     (Python) File 
"/home/siretart/python-biopython/.pybuild/cpython3_3.12/build/Bio/Align/analysis.py", 
line 484, in _yn00
         P = expm(Q * t)
     (Python) File 
"/usr/lib/python3/dist-packages/scipy/linalg/_matfuncs.py", line 358, in 
expm
         eAw = eAw @ eAw

I think that indicates that the problematic / looping test is indeed 
Align_condonalign.py?

-rt