Test failures on musl with python 3.10

[SoapGentoo]

I'm reporting this from Gentoo: https://bugs.gentoo.org/836857

I'm updating Gentoo's pysam to 0.20.0 and tested musl again. This is on musl 1.2.3 with python 3.10.10:

tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works Fatal Python error: Segmentation fault

Current thread 0x00007f1922ca4b48 (most recent call first):
  File "/var/tmp/portage/sci-biology/pysam-0.20.0/work/pysam-0.20.0-python3_10/tests/AlignmentFileHeader_test.py", line 197 in tearDown
  File "/usr/lib/python3.10/unittest/case.py", line 552 in _callTearDown
  File "/usr/lib/python3.10/unittest/case.py", line 594 in run
  File "/usr/lib/python3.10/unittest/case.py", line 650 in __call__
  File "/usr/lib/python3.10/site-packages/_pytest/unittest.py", line 330 in runtest
  File "/usr/lib/python3.10/site-packages/_pytest/runner.py", line 167 in pytest_runtest_call
  File "/usr/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3.10/site-packages/_pytest/runner.py", line 260 in <lambda>
  File "/usr/lib/python3.10/site-packages/_pytest/runner.py", line 339 in from_call
  File "/usr/lib/python3.10/site-packages/_pytest/runner.py", line 259 in call_runtest_hook
  File "/usr/lib/python3.10/site-packages/_pytest/runner.py", line 220 in call_and_report
  File "/usr/lib/python3.10/site-packages/_pytest/runner.py", line 131 in runtestprotocol
  File "/usr/lib/python3.10/site-packages/_pytest/runner.py", line 112 in pytest_runtest_protocol
  File "/usr/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3.10/site-packages/_pytest/main.py", line 349 in pytest_runtestloop
  File "/usr/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3.10/site-packages/_pytest/main.py", line 324 in _main
  File "/usr/lib/python3.10/site-packages/_pytest/main.py", line 270 in wrap_session
  File "/usr/lib/python3.10/site-packages/_pytest/main.py", line 317 in pytest_cmdline_main
  File "/usr/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3.10/site-packages/_pytest/config/__init__.py", line 167 in main
  File "/usr/lib/python3.10/site-packages/_pytest/config/__init__.py", line 190 in console_main
  File "/usr/lib/python3.10/site-packages/pytest/__main__.py", line 5 in <module>
  File "/usr/lib/python3.10/runpy.py", line 86 in _run_code
  File "/usr/lib/python3.10/runpy.py", line 196 in _run_module_as_main

Extension modules: pysam.libcutils, pysam.libchtslib, pysam.libcsamtools, pysam.libcbcftools, pysam.libcfaidx, pysam.libctabixproxies, pysam.libctabix, pysam.libcalignmentfile, pysam.libcalignedsegment, pysam.libcsamfile, pysam.libcvcf, pysam.libcbcf, pysam.libcbgzf, Cython.Plex.Actions, Cython.Plex.Scanners, Cython.Compiler.Scanning, Cython.Tempita._tempita, Cython.Compiler.Visitor, Cython.Compiler.FlowControl, _compile_test (total: 20)
/var/tmp/portage/sci-biology/pysam-0.20.0/temp/environment: line 2050: 512521 Segmentation fault      (core dumped) "${@}"

Samtools and bcftools are both at 1.16.1 and 1.16.

[jmarshall]

Thanks for the bug report. This turns out to be a use-after-free(3) problem, which presumably musl is doing more to facilitate discovery of than some other libc implementations.

[SoapGentoo]

Tested it with HEAD from git, works now, thanks!