* bug#49467: python-scanpy 1.7.2 tests failing with SIGILL
@ 2021-07-08 17:53 Ludovic Courtès
2023-10-04 3:41 ` Maxim Cournoyer
0 siblings, 1 reply; 2+ messages in thread
From: Ludovic Courtès @ 2021-07-08 17:53 UTC (permalink / raw)
To: 49467
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’.
^ permalink raw reply [flat|nested] 2+ messages in thread
* bug#49467: python-scanpy 1.7.2 tests failing with SIGILL
2021-07-08 17:53 bug#49467: python-scanpy 1.7.2 tests failing with SIGILL Ludovic Courtès
@ 2023-10-04 3:41 ` Maxim Cournoyer
0 siblings, 0 replies; 2+ messages in thread
From: Maxim Cournoyer @ 2023-10-04 3:41 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: 49467-done
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
^ permalink raw reply [flat|nested] 2+ messages in thread
end of thread, other threads:[~2023-10-04 3:42 UTC | newest]
Thread overview: 2+ messages (download: mbox.gz / follow: Atom feed)
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2021-07-08 17:53 bug#49467: python-scanpy 1.7.2 tests failing with SIGILL Ludovic Courtès
2023-10-04 3:41 ` Maxim Cournoyer
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