Bug 2463423

Summary:	Substitute use of non-API R function SET_S4_OBJECT
Product:	[Fedora] Fedora	Reporter:	Iñaki Ucar <i.ucar86>
Component:	swig	Assignee:	Jitka Plesnikova <jplesnik>
Status:	CLOSED ERRATA	QA Contact:	Fedora Extras Quality Assurance <extras-qa>
Severity:	medium	Docs Contact:
Priority:	unspecified
Version:	rawhide	CC:	besser82, jplesnik, jskarvad, mjg, zbyszek
Target Milestone:	---
Target Release:	---
Hardware:	Unspecified
OS:	Linux
Whiteboard:
Fixed In Version:	swig-4.4.1-6.fc45 swig-4.4.1-4.fc44	Doc Type:	---
Doc Text:		Story Points:	---
Clone Of:		Environment:
Last Closed:	2026-06-03 11:16:58 UTC	Type:	---
Regression:	---	Mount Type:	---
Documentation:	---	CRM:
Verified Versions:		Category:	---
oVirt Team:	---	RHEL 7.3 requirements from Atomic Host:
Cloudforms Team:	---	Target Upstream Version:
Embargoed:

Description Iñaki Ucar 2026-04-28 10:56:47 UTC

Both graphviz and libsbml, which use swig to build R wrappers, break with the latest R release (4.6), because swig produces code that doesn't adhere to the API. I patched both of them in order to rebuild them, but we would need to fix swig instead.

Particularly, R core has been cleaning the exported C API, and R v4.6.0 (released last Friday) removes a lot of non-API functions. Swig still uses SET_S4_OBJECT, which produces code that doesn't compile under this release. These calls should be replaced with Rf_asS4.

Reproducible: Always

Comment 1 Iñaki Ucar 2026-04-28 11:01:14 UTC

Adding the link to the upstream report.
Adding also the maintainers of the affected packages (libsbml, graphviz) to CC for awareness.

Comment 2 Fedora Update System 2026-06-03 11:14:25 UTC

FEDORA-2026-e253a19ffc (swig-4.4.1-6.fc45) has been submitted as an update to Fedora 45.
https://bodhi.fedoraproject.org/updates/FEDORA-2026-e253a19ffc

Comment 3 Fedora Update System 2026-06-03 11:16:58 UTC

FEDORA-2026-e253a19ffc (swig-4.4.1-6.fc45) has been pushed to the Fedora 45 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 4 Fedora Update System 2026-06-05 12:19:41 UTC

FEDORA-2026-508758c64f (swig-4.4.1-4.fc44) has been submitted as an update to Fedora 44.
https://bodhi.fedoraproject.org/updates/FEDORA-2026-508758c64f

Comment 5 Fedora Update System 2026-06-06 01:24:58 UTC

FEDORA-2026-508758c64f has been pushed to the Fedora 44 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2026-508758c64f`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2026-508758c64f

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 6 Fedora Update System 2026-06-07 00:56:37 UTC

FEDORA-2026-508758c64f (swig-4.4.1-4.fc44) has been pushed to the Fedora 44 stable repository.
If problem still persists, please make note of it in this bug report.