bug#49467: python-scanpy 1.7.2 tests failing with SIGILL

[Maxim Cournoyer]

Hi Ludo,

Ludovic Courtès <ludovic.courtes@inria.fr> writes:

> On an x86_64 machine, I’ve seen this:
>
> $ guix build python-scanpy --no-grafts --check
>
> […]
>
> starting phase `check'
> ============================= test session starts 
> ==============================
> platform linux -- Python 3.8.2, pytest-5.3.5, py-1.8.1, pluggy-0.13.1
> rootdir: /tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2
> plugins: hypothesis-5.4.1, cov-2.8.1, black-0.3.8
> Fatal Python error: Illegal instruction
>
> Current thread 0x00007ffff785c300 (most recent call first):
>   File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
>   File "<frozen importlib._bootstrap_external>", line 1109 in exec_module
>   File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
>   File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
>   File "<frozen importlib._bootstrap>", line 991 in _find_and_load
>   File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
>   File "<frozen importlib._bootstrap>", line 1042 in _handle_fromlist
>   File 
> "/gnu/store/368d0i579ga5sbc3mms4bg7bd4lzj6km-python-numcodecs-0.6.4/lib/python3.8/site-packages/numcodecs/__init

[...]

>   File 
> "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/runner.py",
>  line 237 in from_call
>   File 
> "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/runner.py",
>  line 257 in pytest_make_collect_report
>   File 
> "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/lib/python3.8/site-packages/pluggy/callers.py",
>  line 187 in _multicall
>   File 
> "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/lib/python3.8/site-packages/pluggy/manager.py",
>  line 84 in <lambda>
>   File 
> "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/lib/python3.8/site-packages/pluggy/manager.py",
>  line 93 in _hookexec
>   File 
> "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/lib/python3.8/site-packages/pluggy/hooks.py",
>  line 286 in __call__
>   File 
> "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/runner.py",
>  line 379 in collect_one_node
>   ...
> command "pytest" failed with signal 4
> builder for 
> `/gnu/store/xdqc4a2xhkiknasj8rk36gl3gr5iswr8-python-scanpy-1.7.2.drv' failed 
> with exit code 1
> build of /gnu/store/xdqc4a2xhkiknasj8rk36gl3gr5iswr8-python-scanpy-1.7.2.drv 
> failed
>
> It would seem that one of these dependencies has code using x86_64 ISA
> extensions that this particular CPU doesn’t support.
>
> Thoughts?

I don't reproduce with
/gnu/store/0ch25pmwnxl8vfdwiqz3rk9n4hmmhj39-python-scanpy-1.9.1 on an
old x86_64 CPU (Intel Q6700).

I'm assuming for the best and closing :-)

-- 
Thanks,
Maxim