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

[Ludovic Courtès]

On an x86_64 machine, I’ve seen this:

--8<---------------cut here---------------start------------->8---
$ 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
__.py", line 45 in <module>
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 783 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 
"/gnu/store/cjclqalblsxf8l6cn1l1r4qmyjab0di3-python-zarr-2.4.0/lib/python3.8/site-packages/zarr/codecs.py",
 line
 3 in <module>
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 783 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 
"/gnu/store/cjclqalblsxf8l6cn1l1r4qmyjab0di3-python-zarr-2.4.0/lib/python3.8/site-packages/zarr/__init__.py",
 li
ne 3 in <module>
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 783 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 961 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 991 in _find_and_load
  File 
"/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/compat/__i
nit__.py", line 19 in <module>
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 783 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 
"/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/_core/views.py",
 line 13 in <module>
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 783 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 
"/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/_core/aligned_mapping.py",
 line 13 in <module>
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 783 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 
"/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/_core/raw.py",
 line 11 in <module>
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 783 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 
"/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/_core/anndata.py",
 line 26 in <module>
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 783 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 
"/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/__init__.py",
 line 7 in <module>
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 783 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 
"/tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2/scanpy/_utils.py", line 
18 in <module>
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 783 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 
"/tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2/scanpy/__init__.py", 
line 5 in <module>
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 783 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 
"/tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2/scanpy/tests/conftest.py",
 line 11 in <module>
  File 
"/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/assertion/rewrite.py",
 line 143 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 
"/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/python3.8/site-packages/py/_path/local.py",
 line 701 in pyimport
  File 
"/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/config/__init__.py",
 line 465 in _importconftest
  File 
"/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/config/__init__.py",
 line 437 in _getconftestmodules
  File 
"/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/main.py",
 line 445 in gethookproxy
  File 
"/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/main.py",
 line 626 in _recurse
  File 
"/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/python3.8/site-packages/py/_path/common.py",
 line 425 in <listcomp>
  File 
"/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/python3.8/site-packages/py/_path/common.py",
 line 424 in gen
  File 
"/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/python3.8/site-packages/py/_path/common.py",
 line 435 in gen
  File 
"/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/python3.8/site-packages/py/_path/common.py",
 line 383 in visit
  File 
"/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/main.py",
 line 545 in _collect
  File 
"/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/main.py",
 line 504 in collect
  File 
"/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/runner.py",
 line 257 in <lambda>
  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
--8<---------------cut here---------------end--------------->8---

It would seem that one of these dependencies has code using x86_64 ISA
extensions that this particular CPU doesn’t support.

Thoughts?

Ludo’.