Unspecified test error in 2.10.3 `Fatal Python error: Aborted`

[TheChymera]

I am getting an error when trying to run the test suite for =zarr-2.10.3 which I can't really understand.

Here is the full build log

The actual failure seen towards the bottom is:

/var/tmp/portage/dev-python/zarr-2.10.3/temp/environment: line 1689:    70 Aborted                 "${@}"

[joshmoore]

The fact that the failure occurs on chunk encoding:

Current thread 0x00007f4b9099cb80 (most recent call first):
  File "/var/tmp/portage/dev-python/zarr-2.10.3/work/zarr-2.10.3/zarr/core.py", line 2012 in _encode_chunk

suggests that there's an issue with your installation of numcodecs. How did you install/build the zarr dependencies?

[TheChymera]

@joshmoore thank you for replying to this. There is indeed an issue with numcodecs (it appears to build fine, but some of the tests fail).

This is the full build and test log for numcodecs. I have also reported the numcodecs issue, but there has yet to be any feedback on it.

[TheChymera]

@joshmoore I went over this again, and this is the list of tests that fail (interestingly, for some reason, pytest got stuck on each and every one of them, and didn't just go through the whole suite collecting the failures).

    zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes
    zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes
    zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes
    zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes
    zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes
    zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes
    zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes
    zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes
    zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes
    zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes
    zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes
    zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes
    zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes
    zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes
    zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes
    zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes
    zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes

It seems test_object_arrays_vlen_bytes is the common denominator. Any idea if this can help us figure out what's wrong (and possibly indirectly help figure out what's up with the unresolved numcodecs error)?

[joshmoore]

pytest got stuck on each and every one of them

Any chance of getting a backtrace (e.g. with gdb)?

[jhamman]

I'm guessing this has been fixed or is no longer an issue. @TheChymera - feel free to reopen if I've got that wrong.