Bug 1994181
| Summary: | python-tables fails to build with hdf5 1.10.7 | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Orion Poplawski <orion> |
| Component: | python-tables | Assignee: | Thibault North <thibault> |
| Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | urgent | Docs Contact: | |
| Priority: | unspecified | ||
| Version: | 35 | CC: | dave.love, thibault, zbyszek |
| Target Milestone: | --- | ||
| Target Release: | --- | ||
| Hardware: | Unspecified | ||
| OS: | All | ||
| Whiteboard: | |||
| Fixed In Version: | python-tables-3.6.1-12.fc35 | Doc Type: | If docs needed, set a value |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2021-09-30 00:52:19 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: | 2004456 | ||
In case it helps, this is probably something specific to the Fedora-spacific build. As I have a user struggling with this stuff (not the rpm packaging), I tried the Spack py-tables package, which reported its tests passed with tables 3.6.1 and hdf5 1.10.7 (and python 3.8). (I only saw an upstream report for a later hdf5, but that was left asking for more info about the installation.) FEDORA-2021-666c16e918 has been submitted as an update to Fedora 35. https://bodhi.fedoraproject.org/updates/FEDORA-2021-666c16e918 A buildroot override has also been submitted: $ koji wait-repo f35-build --build=python-tables-3.6.1-12.fc35 FEDORA-2021-666c16e918 has been pushed to the Fedora 35 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --advisory=FEDORA-2021-666c16e918` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2021-666c16e918 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates. FEDORA-2021-666c16e918 has been pushed to the Fedora 35 stable repository. If problem still persists, please make note of it in this bug report. |
Description of problem: python-tables appears to not be compatible with hdf5 1.10.7 for some reason. Tests fail with: ERROR: test00_attributes (tables.tests.test_vlarray.Fletcher32TestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILDROOT/python-tables-3.6.1-5.fc35.x86_64/usr/lib64/python3.10/site-packages/tables/tests/test_vlarray.py", line 37, in setUp self.populateFile() File "/builddir/build/BUILDROOT/python-tables-3.6.1-5.fc35.x86_64/usr/lib64/python3.10/site-packages/tables/tests/test_vlarray.py", line 47, in populateFile vlarray = self.h5file.create_vlarray(group, 'vlarray1', File "/builddir/build/BUILDROOT/python-tables-3.6.1-5.fc35.x86_64/usr/lib64/python3.10/site-packages/tables/file.py", line 1493, in create_vlarray ptobj = VLArray(parentnode, name, File "/builddir/build/BUILDROOT/python-tables-3.6.1-5.fc35.x86_64/usr/lib64/python3.10/site-packages/tables/vlarray.py", line 349, in __init__ super(VLArray, self).__init__(parentnode, name, new, filters, File "/builddir/build/BUILDROOT/python-tables-3.6.1-5.fc35.x86_64/usr/lib64/python3.10/site-packages/tables/leaf.py", line 286, in __init__ super(Leaf, self).__init__(parentnode, name, _log) File "/builddir/build/BUILDROOT/python-tables-3.6.1-5.fc35.x86_64/usr/lib64/python3.10/site-packages/tables/node.py", line 264, in __init__ self._v_objectid = self._g_create() File "/builddir/build/BUILDROOT/python-tables-3.6.1-5.fc35.x86_64/usr/lib64/python3.10/site-packages/tables/vlarray.py", line 419, in _g_create self._v_objectid = self._create_array(self._v_new_title) File "tables/hdf5extension.pyx", line 1968, in tables.hdf5extension.VLArray._create_array raise HDF5ExtError("Problems creating the VLArray.") tables.exceptions.HDF5ExtError: HDF5 error back trace File "../../src/H5D.c", line 152, in H5Dcreate2 unable to create dataset File "../../src/H5Dint.c", line 338, in H5D__create_named unable to create and link to dataset File "../../src/H5L.c", line 1605, in H5L_link_object unable to create new link to object File "../../src/H5L.c", line 1846, in H5L__create_real can't insert link File "../../src/H5Gtraverse.c", line 848, in H5G_traverse internal path traversal failed File "../../src/H5Gtraverse.c", line 624, in H5G__traverse_real traversal operator failed File "../../src/H5L.c", line 1652, in H5L__link_cb unable to create object File "../../src/H5Oint.c", line 2496, in H5O_obj_create unable to open object File "../../src/H5Doh.c", line 300, in H5O__dset_create unable to create dataset File "../../src/H5Dint.c", line 1230, in H5D__create H5Z_has_optional_filter() failed File "../../src/H5Z.c", line 1060, in H5Z_ignore_filters not suitable for filters End of HDF5 error back trace Problems creating the VLArray. Version-Release number of selected component (if applicable): python-tables-3.6.1-5 Problem has been reported upstream, but no action there yet.