Bug 2128592 - libsbml tests fails with SWIG 4.1.0
Summary: libsbml tests fails with SWIG 4.1.0
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: libsbml
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Zbigniew Jędrzejewski-Szmek
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2022-09-21 08:04 UTC by Jitka Plesnikova
Modified: 2022-09-22 18:32 UTC (History)
4 users (show)

Fixed In Version: libsbml-5.19.0-20.fc38
Clone Of:
Environment:
Last Closed: 2022-09-22 18:32:26 UTC
Type: Bug
Embargoed:

Attachments (Terms of Use)
Fix for SWIG 4.1.0 (687 bytes, patch)
2022-09-21 08:04 UTC, Jitka Plesnikova 		no flags Details | Diff
View All

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.
Note You need to log in before you can comment on or make changes to this bug.