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
