Bug 32961 - kalzium fails due issue in avogadrolibs
Summary: kalzium fails due issue in avogadrolibs
Status: RESOLVED FIXED
Alias: None
Product: Mageia
Classification: Unclassified
Component: RPM Packages (show other bugs)
Version: 9
Hardware: All Linux
Priority: Normal normal
Target Milestone: ---
Assignee: QA Team
QA Contact:
URL: https://github.com/OpenChemistry/avog...
Whiteboard: MGA9-64-OK,MGA9-32-OK
Keywords: advisory, validated_update
Depends on: 32953
Blocks:
  Show dependency tree / graph
 
Reported: 2024-03-12 19:33 CET by katnatek
Modified: 2024-03-22 02:42 CET (History)
5 users (show)

See Also:
Source RPM: avogadrolibs,avogadro2
CVE:
Status comment:

Attachments
Add an attachment (proposed patch, testcase, etc.)

Description katnatek 2024-03-12 19:33:44 CET 
From bug#32953 comment#22
David GEIGER 2024-03-11 11:08:24 CST

(In reply to Ben McMonagle from comment #18)
> not sure what to make of this one:
> there are 2 kalzium .desktop entries.
> 
> org.kde.kalzium_cml.desktop
> org.kde.kalzium.desktop
> 
> one entry in application menu.
> 
> org.kde.kalzium.desktop
> $kalzium
> 
> works fine every time.
> 
> org.kde.kalzium_cml.desktop
> $ kalzium -qwindowtitle %c -molecule %f
> Segmentation fault (core dumped)
> 
> 4 out of 5 times ( on different hardware / intel & amd CPUs ) above result.
> 1 out of 5 times works fine.
> 
> users would not normally use the above command.

Apparently this issue come from avogadrolibs and not kalzium itself:

https://bugs.kde.org/show_bug.cgi?id=457191
https://github.com/OpenChemistry/avogadrolibs/issues/1193


Should be fixed now with new avogadrolibs-1.99.0-1.mga9 update:

Packages in 9/Core/Updates_testing:
======================
avogadro2-1.99.0-1.mga9

avogadrolibs-1.99.0-1.mga9
lib64avogadrocalc1-1.99.0-1.mga9
lib64avogadrocore1-1.99.0-1.mga9
lib64avogadroio1-1.99.0-1.mga9
lib64avogadrolibs-devel-1.99.0-1.mga9
lib64avogadromolequeue1-1.99.0-1.mga9
lib64avogadroqtgui1-1.99.0-1.mga9
lib64avogadroqtopengl1-1.99.0-1.mga9
lib64avogadroqtplugins1-1.99.0-1.mga9
lib64avogadroquantumio1-1.99.0-1.mga9
lib64avogadrorendering1-1.99.0-1.mga9
libavogadrocalc1-1.99.0-1.mga9
libavogadrocore1-1.99.0-1.mga9
libavogadroio1-1.99.0-1.mga9
libavogadrolibs-devel-1.99.0-1.mga9
libavogadromolequeue1-1.99.0-1.mga9
libavogadroqtgui1-1.99.0-1.mga9
libavogadroqtopengl1-1.99.0-1.mga9
libavogadroqtplugins1-1.99.0-1.mga9
libavogadroquantumio1-1.99.0-1.mga9
libavogadrorendering1-1.99.0-1.mga9


From SRPMS:
avogadrolibs-1.99.0-1.mga9.src.rpm
avogadro2-1.99.0-1.mga9.src.rpm
katnatek 2024-03-12 19:35:28 CET

Source RPM: (none) => avogadrolibs,avogadro2

katnatek 2024-03-12 19:42:38 CET

CC: (none) => andrewsfarm

katnatek 2024-03-12 19:43:46 CET

Keywords: (none) => advisory

katnatek 2024-03-12 19:44:11 CET

CC: (none) => westel

Comment 1 katnatek 2024-03-12 19:45:41 CET 
Ben McMonagle, can you confirm these packages fix the issue you detect with 
kalzium +"molecule button"
Comment 2 Ben McMonagle 2024-03-12 21:43:32 CET 
Installed packages.

unfortunately, issue still apparent.
Comment 3 David GEIGER 2024-03-12 23:26:24 CET 
So ok we have to rebuild kalzium against new avogradolibs:

New packages in 9/Core/Updates_testing:
=========================
kalzium-23.04.3-1.1.mga9
kalzium-devel-23.04.3-1.1.mga9
kalzium-handbook-23.04.3-1.1.mga9.noarch.rpm
lib64compoundviewer5-23.04.3-1.1.mga9
lib64science5-23.04.3-1.1.mga9

libcompoundviewer5-23.04.3-1.1.mga9
libscience5-23.04.3-1.1.mga9

From SRPMS:
kalzium-23.04.3-1.1.mga9.src.rpm

CC: (none) => geiger.david68210

Comment 4 Ben McMonagle 2024-03-12 23:45:19 CET 
(In reply to Ben McMonagle from comment #2)
> Installed packages.
> 
> unfortunately, issue still apparent.

]$ kalzium -qwindowtitle %c -molecule %f
double free or corruption (out)
Aborted (core dumped)
Comment 5 Ben McMonagle 2024-03-12 23:45:54 CET 
(In reply to David GEIGER from comment #3)
> So ok we have to rebuild kalzium against new avogradolibs:
> 
> New packages in 9/Core/Updates_testing:
> =========================
> kalzium-23.04.3-1.1.mga9
> kalzium-devel-23.04.3-1.1.mga9
> kalzium-handbook-23.04.3-1.1.mga9.noarch.rpm
> lib64compoundviewer5-23.04.3-1.1.mga9
> lib64science5-23.04.3-1.1.mga9
> 
> libcompoundviewer5-23.04.3-1.1.mga9
> libscience5-23.04.3-1.1.mga9
> 
> From SRPMS:
> kalzium-23.04.3-1.1.mga9.src.rpm

will await the update in due course.
Comment 6 Ben McMonagle 2024-03-13 12:51:30 CET 
installed into my real 32bit system tonight as part of plasma update testing.

amd xp2400+ processor.

clicking the "molecule" button does not cause the application to crash.

will update and check a 64bit tomorrow. (after midnight here)
Comment 7 Ben McMonagle 2024-03-13 20:32:37 CET 
updated 64bit system today to kalzium-23.04.3-1.1.mga9


issue resolved
katnatek 2024-03-13 20:38:00 CET

Whiteboard: (none) => MGA9-64-OK,MGA9-32-OK

Comment 8 katnatek 2024-03-13 20:40:00 CET 
 David GEIGER  this must wait until bug#32953 is validated?
Comment 9 David GEIGER 2024-03-13 20:41:18 CET 
Yes this should part of the big kde-gears update!
katnatek 2024-03-14 03:13:52 CET

Depends on: (none) => 32953

Comment 10 katnatek 2024-03-19 17:09:58 CET 
This need to be validated to not have issues with kalzium

Keywords: (none) => validated_update
CC: (none) => sysadmin-bugs

Comment 11 Dan Fandrich 2024-03-22 01:26:10 CET 
#32953 has now been submitted. Does that mean this is ready to go or does it need more testing?

CC: (none) => dan

Comment 12 katnatek 2024-03-22 02:12:46 CET 
(In reply to Dan Fandrich from comment #11)
> #32953 has now been submitted. Does that mean this is ready to go or does it
> need more testing?

No more testing is needed, Ben who discover the bug test in both arches in comment#6 and comment#7, please move this packages ASAP, or we can receive unnecessary bug reports about kalzium
Comment 13 Mageia Robot 2024-03-22 02:32:32 CET 
An update for this issue has been pushed to the Mageia Updates repository.

https://advisories.mageia.org/MGAA-2024-0113.html

Resolution: (none) => FIXED
Status: NEW => RESOLVED

Comment 14 katnatek 2024-03-22 02:42:30 CET 
Thank you Dan
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