Bug 2339472 - openbabel fails to build with Python 3.14: test_align_4 and test_align_5 fail
Summary: openbabel fails to build with Python 3.14: test_align_4 and test_align_5 fail
Keywords:
Status: NEW
Alias: None
Product: Fedora
Classification: Fedora
Component: openbabel
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Antonio T. sagitter
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: PYTHON3.14
TreeView+ depends on / blocked
 
Reported: 2025-01-22 15:25 UTC by Karolina Surma
Modified: 2025-03-31 10:34 UTC (History)
6 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed:
Type: Bug
Embargoed:


Attachments (Terms of Use)

Description Karolina Surma 2025-01-22 15:25:39 UTC
openbabel fails to build with Python 3.14.0a4.

  4/225 Test   #4: test_align_4 .....................***Failed  Error regular expression found in output. Regex=[FAIL]  0.10 sec
==============================
*** Open Babel Error  in Align
  Cannot align the reference and target as they are of different size
==============================
*** Open Babel Error  in GetRMSD
  RMSD not available until you call Align()
/builddir/build/BUILD/openbabel-3.1.1-build/openbabel-openbabel-3-1-1/test/aligntest.cpp:183: fabs(rmsd) > 1.0E-2 (FAIL)

        Start   5: test_align_5
  5/225 Test   #5: test_align_5 .....................Subprocess aborted***Exception:   0.14 sec
==============================
*** Open Babel Error  in Align
  Cannot align the reference and target as they are of different size
==============================
*** Open Babel Error  in GetRMSD
  RMSD not available until you call Align()
/builddir/build/BUILD/openbabel-3.1.1-build/openbabel-openbabel-3-1-1/test/aligntest.cpp:221: fabs(rmsd) > 1.0E-3 (FAIL)
==============================
*** Open Babel Error  in GetAlignment
  Alignment not available until you call Align()
/builddir/build/BUILD/openbabel-3.1.1-build/openbabel-openbabel-3-1-1/test/aligntest.cpp:223: result.size() == mol.NumAtoms() (FAIL)
==============================
*** Open Babel Error  in Align
  Cannot align the reference and target as they are of different size
==============================
*** Open Babel Error  in GetRMSD
  RMSD not available until you call Align()
/builddir/build/BUILD/openbabel-3.1.1-build/openbabel-openbabel-3-1-1/test/aligntest.cpp:229: fabs(rmsd) < 1.0E-6 (FAIL)
==============================
*** Open Babel Error  in GetAlignment
  Alignment not available until you call Align()
/builddir/build/BUILD/openbabel-3.1.1-build/openbabel-openbabel-3-1-1/test/aligntest.cpp:231: result.size() == mol.NumAtoms() (FAIL)

https://docs.python.org/3.14/whatsnew/3.14.html

For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/@python/python3.14/fedora-rawhide-x86_64/08554838-openbabel/

For all our attempts to build openbabel with Python 3.14, see:
https://copr.fedorainfracloud.org/coprs/g/python/python3.14/package/openbabel/

Testing and mass rebuild of packages is happening in copr.
You can follow these instructions to test locally in mock if your package builds with Python 3.14:
https://copr.fedorainfracloud.org/coprs/g/python/python3.14/

Let us know here if you have any questions.

Python 3.14 is planned to be included in Fedora 43.
To make that update smoother, we're building Fedora packages with all pre-releases of Python 3.14.
A build failure prevents us from testing all dependent packages (transitive [Build]Requires),
so if this package is required a lot, it's important for us to get it fixed soon.

We'd appreciate help from the people who know this package best,
but if you don't want to work on this now, let us know so we can try to work around it on our side.

Comment 1 Aoife Moloney 2025-02-26 13:25:20 UTC
This bug appears to have been reported against 'rawhide' during the Fedora Linux 42 development cycle.
Changing version to 42.


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