Bug 2244500
| Summary: | Many python-pypet tests fail on s390x due to apparent endian issues in pandas.HDFStore | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Ben Beasley <code> |
| Component: | python-pypet | Assignee: | Orphan Owner <extras-orphan> |
| Status: | CLOSED EOL | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | unspecified | Docs Contact: | |
| Priority: | unspecified | ||
| Version: | 40 | CC: | neuro-sig, sanjay.ankur |
| Target Milestone: | --- | ||
| Target Release: | --- | ||
| Hardware: | Unspecified | ||
| OS: | Unspecified | ||
| Whiteboard: | |||
| Fixed In Version: | Doc Type: | If docs needed, set a value | |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2025-05-16 07:45:36 UTC | Type: | Bug |
| Regression: | --- | Mount Type: | --- |
| Documentation: | --- | CRM: | |
| Verified Versions: | Category: | --- | |
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |
| Cloudforms Team: | --- | Target Upstream Version: | |
| Embargoed: | |||
| Bug Depends On: | |||
| Bug Blocks: | 485231 | ||
This is very likely the same bug described in: https://src.fedoraproject.org/rpms/python-pandas/blob/c29517a7d496f6fc200f55725de4223746c2b2de/f/python-pandas.spec#_631 This bug appears to have been reported against 'rawhide' during the Fedora Linux 40 development cycle. Changing version to 40. This package has changed maintainer in Fedora. Reassigning to the new maintainer of this component. This message is a reminder that Fedora Linux 40 is nearing its end of life. Fedora will stop maintaining and issuing updates for Fedora Linux 40 on 2025-05-13. It is Fedora's policy to close all bug reports from releases that are no longer maintained. At that time this bug will be closed as EOL if it remains open with a 'version' of '40'. Package Maintainer: If you wish for this bug to remain open because you plan to fix it in a currently maintained version, change the 'version' to a later Fedora Linux version. Note that the version field may be hidden. Click the "Show advanced fields" button if you do not see it. Thank you for reporting this issue and we are sorry that we were not able to fix it before Fedora Linux 40 is end of life. If you would still like to see this bug fixed and are able to reproduce it against a later version of Fedora Linux, you are encouraged to change the 'version' to a later version prior to this bug being closed. Fedora Linux 40 entered end-of-life (EOL) status on 2025-05-13. Fedora Linux 40 is no longer maintained, which means that it will not receive any further security or bug fix updates. As a result we are closing this bug. If you can reproduce this bug against a currently maintained version of Fedora Linux please feel free to reopen this bug against that version. Note that the version field may be hidden. Click the "Show advanced fields" button if you do not see the version field. If you are unable to reopen this bug, please file a new report against an active release. Thank you for reporting this bug and we are sorry it could not be fixed. |
While working to improve packaging and testing of the python-pypet package, I found that very many tests (approximately half) fail due to apparent endian issues in pandas.HDFStore. Here is a typical example: ====================================================================== ERROR: test_storage_and_loading (unittests.annotations_test.AnnotationsTest.test_storage_and_loading) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILDROOT/python-pypet-0.5.2-30.fc40.s390x/usr/lib/python3.12/site-packages/pypet/tests/unittests/annotations_test.py", line 94, in test_storage_and_loading self.traj.f_store() File "/builddir/build/BUILDROOT/python-pypet-0.5.2-30.fc40.s390x/usr/lib/python3.12/site-packages/pypet/utils/decorators.py", line 163, in new_func return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-pypet-0.5.2-30.fc40.s390x/usr/lib/python3.12/site-packages/pypet/utils/decorators.py", line 163, in new_func return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-pypet-0.5.2-30.fc40.s390x/usr/lib/python3.12/site-packages/pypet/utils/decorators.py", line 121, in new_func return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-pypet-0.5.2-30.fc40.s390x/usr/lib/python3.12/site-packages/pypet/trajectory.py", line 2872, in f_store self._storage_service.store(pypetconstants.TRAJECTORY, self, File "/builddir/build/BUILDROOT/python-pypet-0.5.2-30.fc40.s390x/usr/lib/python3.12/site-packages/pypet/storageservice.py", line 1337, in store self._srvc_closing_routine(opened) File "/builddir/build/BUILDROOT/python-pypet-0.5.2-30.fc40.s390x/usr/lib/python3.12/site-packages/pypet/storageservice.py", line 1556, in _srvc_closing_routine os.fsync(f_fd) OverflowError: Python int too large to convert to C int I suspect the file descriptor is being loaded from HDF5 with the wrong endianness. I can’t find anywhere this would be happening in pypet; I think it is a pandas.HDFStore bug. Note that pandas does not test big-endian support but will happily accept patches to improve it: https://github.com/pandas-dev/pandas/issues/4737#issuecomment-1090931741 For now, I plan to add “ExcludeArch: s390x” to python-pypet. This bug is the tracking bug required under https://docs.fedoraproject.org/en-US/packaging-guidelines/#_architecture_build_failures.