Hi Reinhard, Reinhard Tartler, on 2024-08-24: > 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:
This is a very handy tool and I need to recall about it when I'll next need it, probably too soon for my taste. :) […] > (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? This is highly plausible. It was a bold assumption from me to believe the standard output would be flushed to let us see whether the test started. The stack trace is even pointing to something off in scipy/linalg/_matfunc.py, even more so as scipy is only suggested by python3-biopython, so it is not available in the lightweight variant of the autopkgtest, which does run the test_Align_codonalign.py but doesn't hangup. And indeed, here is what I see in test_Align_codonalign.py, starting line 8235: try: import scipy except ImportError: # Silently skip the rest of the test return My current conclusion is: it seems to me that Biopython's test suite revealed something off in SciPy specifically on Risc-V. Have a nice day, :) -- .''`. Étienne Mollier <emoll...@debian.org> : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/1, please excuse my verbosity `-
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