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Segfault in numcodecs/tests/test_vlen_bytes.py::test_encode_none #735
Description
I run the unit test suite in debian sid (x86_64) i get a segmentation fault:
python3.13 -m pytes -v --pyargs numcodecs
============================= test session starts ==============================
platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3.13
cachedir: .pytest_cache
rootdir: /build/numcodecs-0.16.0+ds/.pybuild/cpython3_3.13_numcodecs/build
configfile: pyproject.toml
plugins: typeguard-4.4.2, cov-5.0.0
collecting ... collected 698 items / 27 deselected / 4 skipped / 671 selected
numcodecs/astype.py::numcodecs.astype.AsType PASSED [ 0%]
[...]
numcodecs/tests/test_vlen_bytes.py::test_decode_errors PASSED [ 96%]
numcodecs/tests/test_vlen_bytes.py::test_encode_none Fatal Python error: Aborted
Current thread 0x00007ebfefa2e100 (most recent call first):
File "/build/numcodecs-0.16.0+ds/.pybuild/cpython3_3.13_numcodecs/build/numcodecs/tests/test_vlen_bytes.py", line 94 in test_encode_none
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159 in pytest_pyfunc_call
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627 in runtest
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174 in pytest_runtest_call
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242 in <lambda>
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341 in from_call
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 241 in call_and_report
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 132 in runtestprotocol
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 113 in pytest_runtest_protocol
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 362 in pytest_runtestloop
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 337 in _main
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 283 in wrap_session
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 330 in pytest_cmdline_main
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 175 in main
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 201 in console_main
File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in <module>
File "<frozen runpy>", line 88 in _run_code
File "<frozen runpy>", line 198 in _run_module_as_main
Extension modules: numpy._core._multiarray_umath, numpy.linalg._umath_linalg, numcodecs.compat_ext, numcodecs.blosc, numcodecs.zstd, numcodecs.lz4, numcodecs._shuffle, numcodecs.jenkins, crc32c._crc32c, numcodecs.vlen, numcodecs.fletcher32, msgpack._cmsgpack, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator (total: 21)
Aborted (core dumped)
Activity
jakirkham commentedon Apr 9, 2025
Thanks for the report! 🙏
Are you able to run the test with
gdb(perhaps like so)?jakirkham commentedon Apr 9, 2025
Looks like this happened before on macOS ( #683 )
Appears we had skipped test on macOS in PR: #690
jakirkham commentedon Apr 10, 2025
Was able to reproduce the issue. Did a bit more digging here: #683 (comment)
Came up with a fix that works for me locally in PR: #736
Please try it out and let us know how it goes 🙂
avalentino commentedon Apr 10, 2025
Thanks @jakirkham or the super-fast solution.
I confirm that everything works fine with your patch.
jakirkham commentedon Apr 11, 2025
Thanks Antonio! 🙏
Appreciate the timely retesting
Have gone ahead and merged
This will show up in the next release