Package: guix;
Reported by: Ludovic Courtès <ludovic.courtes <at> inria.fr>
Date: Thu, 8 Jul 2021 17:54:01 UTC
Severity: normal
Done: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
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bug-guix <at> gnu.org:bug#49467; Package guix.
(Thu, 08 Jul 2021 17:54:02 GMT) Full text and rfc822 format available.Ludovic Courtès <ludovic.courtes <at> inria.fr>:bug-guix <at> gnu.org.
(Thu, 08 Jul 2021 17:54:02 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Ludovic Courtès <ludovic.courtes <at> inria.fr> To: bug-guix <at> gnu.org Subject: python-scanpy 1.7.2 tests failing with SIGILL Date: Thu, 08 Jul 2021 19:53:19 +0200
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’.
Maxim Cournoyer <maxim.cournoyer <at> gmail.com>:Ludovic Courtès <ludovic.courtes <at> inria.fr>:Message #10 received at 49467-done <at> debbugs.gnu.org (full text, mbox):
From: Maxim Cournoyer <maxim.cournoyer <at> gmail.com> To: Ludovic Courtès <ludovic.courtes <at> inria.fr> Cc: 49467-done <at> debbugs.gnu.org Subject: Re: bug#49467: python-scanpy 1.7.2 tests failing with SIGILL Date: Tue, 03 Oct 2023 23:41:10 -0400
Hi Ludo, Ludovic Courtès <ludovic.courtes <at> 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
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