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Bug 1705452
| Summary: | rdkit fails to rebuild with Python 3.8 | ||||||
|---|---|---|---|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Miro Hrončok <mhroncok> | ||||
| Component: | rdkit | Assignee: | Gianluca Sforna <giallu> | ||||
| Status: | CLOSED RAWHIDE | QA Contact: | Fedora Extras Quality Assurance <extras-qa> | ||||
| Severity: | unspecified | Docs Contact: | |||||
| Priority: | unspecified | ||||||
| Version: | rawhide | CC: | giallu | ||||
| 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: | 2019-07-13 08:04:54 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: | 1686977 | ||||||
| Attachments: |
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Please respond. As you suspected the test failures are not related to python 3.8. I'm getting different failures on other platforms, some of them reported upstream, but right now I had to disable the tests until all of them are fixed. Without tests the build succeeded, and I updated to the latest upstream release in rawhide |
Created attachment 1561519 [details] Full log from Copr rdkit 2018.09.2-5.fc31 fails to rebuild with Python 3.8 due to test failures. Those might not be Python 3.8 related, but the package needs to rebuild, otherwise it won't be installable once we update Python. 140: ====================================================================== 140: FAIL: testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable (__main__.TestCase) 140: ---------------------------------------------------------------------- 140: Traceback (most recent call last): 140: File "UnitTestMol3D.py", line 218, in testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable 140: self.assertEqual(smiles, expected) 140: AssertionError: Items in the first set but not the second: 140: 'C/C(F)=C/[C@@H](Cl)/C=C(\\Br)[C@H](N)I' 140: 'C/C(F)=C\\[C@H](Cl)/C=C(\\Br)[C@H](N)I' 140: Items in the second set but not the first: 140: 'C/C(F)=C/[C@H](Cl)/C=C(\\Br)[C@H](N)I' 140: 'C/C(F)=C/[C@@H](Cl)/C=C(/Br)[C@@H](N)I' 140: 140: ---------------------------------------------------------------------- 140: ====================================================================== 140: FAIL: EnumerateStereoisomers (rdkit.Chem.EnumerateStereoisomers) 140: Doctest: rdkit.Chem.EnumerateStereoisomers.EnumerateStereoisomers 140: ---------------------------------------------------------------------- 140: Traceback (most recent call last): 140: File "/usr/lib64/python3.8/doctest.py", line 2196, in runTest 140: raise self.failureException(self.format_failure(new.getvalue())) 140: AssertionError: Failed doctest test for rdkit.Chem.EnumerateStereoisomers.EnumerateStereoisomers 140: File "/builddir/build/BUILD/rdkit-Release_2018_09_2/python3/rdkit/Chem/EnumerateStereoisomers.py", line 98, in EnumerateStereoisomers 140: 140: ---------------------------------------------------------------------- 140: File "/builddir/build/BUILD/rdkit-Release_2018_09_2/python3/rdkit/Chem/EnumerateStereoisomers.py", line 210, in rdkit.Chem.EnumerateStereoisomers.EnumerateStereoisomers 140: Failed example: 140: for smi in sorted(Chem.MolToSmiles(x, isomericSmiles=True) for x in isomers): 140: print(smi) 140: Expected: 140: F[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)Br 140: F[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)Br 140: F[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)Br 140: Got: 140: F[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)Br 140: F[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)Br 140: F[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)Br 140: 140: 140: ---------------------------------------------------------------------- Full log attached.