Bug 2128592

Summary: libsbml tests fails with SWIG 4.1.0
Product: [Fedora] Fedora Reporter: Jitka Plesnikova <jplesnik>
Component: libsbmlAssignee: Zbigniew Jędrzejewski-Szmek <zbyszek>
Status: CLOSED ERRATA QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: unspecified Docs Contact:
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Version: rawhideCC: neuro-sig, r-maint-sig, trpost, zbyszek
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Fixed In Version: libsbml-5.19.0-20.fc38 Doc Type: If docs needed, set a value
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Last Closed: 2022-09-22 18:32:26 UTC Type: Bug
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Description Flags
Fix for SWIG 4.1.0 none

Description Jitka Plesnikova 2022-09-21 08:04:57 UTC 
Created attachment 1913277 [details]
Fix for SWIG 4.1.0

I am testing rebuild of SWIG dependencies against upcoming version 4.1.0 in Fedora rawhide/38.

The test of libSBML-5.19.0 is failing with this version.

35: Test command: /usr/bin/python3 "/builddir/build/BUILD/libSBML-5.19.0-Source/examples/python/append_to_note.py" "/builddir/build/BUILD/libSBML-5.19.0-Source/examples/sample-models/from-spec/level-3/enzymekineticext.xml" "veq" "a new note" "append_to_note.out.xml"
35: Working Directory: /builddir/build/BUILD/libSBML-5.19.0-Source/build/src/bindings/python
35: Environment variables: 
35:  PYTHONPATH=/builddir/build/BUILD/libSBML-5.19.0-Source/build/src/bindings/python:/builddir/build/BUILD/libSBML-5.19.0-Source/build/src/bindings/python:
35: Test timeout computed to be: 3000
35: Body before change: 
35: <body xmlns="http://www.w3.org/1999/xhtml">
35:   <p xmlns="http://www.w3.org/1999/xhtml">Some notes</p>
35: </body>
35: Traceback (most recent call last):
35:   File "/builddir/build/BUILD/libSBML-5.19.0-Source/examples/python/append_to_note.py", line 95, in <module>
35:     addToNotes(doc, sys.argv[2], sys.argv[3])
35:   File "/builddir/build/BUILD/libSBML-5.19.0-Source/examples/python/append_to_note.py", line 78, in addToNotes
35:     body.addChild(libsbml.XMLNode_convertStringToXMLNode(stringToAdd))
35:                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
35: AttributeError: module 'libsbml' has no attribute 'XMLNode_convertStringToXMLNode'
35/68 Test #35: test_python_append_to_note ....................***Failed    0.13 sec

Complete build log is https://download.copr.fedorainfracloud.org/results/jplesnik/swig-rebuild/fedora-rawhide-x86_64/04863226-libsbml/builder-live.log.gz

Upstream provides the two possible solution (it is same error as for nordugrid-arc):
https://github.com/swig/swig/issues/2376#issuecomment-1251577548

The attachment contains fix and the solution also works with any older SWIG version.
Comment 1 Fedora Update System 2022-09-22 18:30:49 UTC 
FEDORA-2022-ec4d0ae8ee has been submitted as an update to Fedora 38. https://bodhi.fedoraproject.org/updates/FEDORA-2022-ec4d0ae8ee
Comment 2 Fedora Update System 2022-09-22 18:32:26 UTC 
FEDORA-2022-ec4d0ae8ee has been pushed to the Fedora 38 stable repository.
If problem still persists, please make note of it in this bug report.