Bug 2526051

Summary:	Stuck on "Install pending software updates" on Shutdown/Restart due to dnf offline cache not cleaned
Product:	[Fedora] Fedora	Reporter:	tor
Component:	dnf5	Assignee:	rpm-software-management
Status:	CLOSED DUPLICATE	QA Contact:
Severity:	medium	Docs Contact:
Priority:	unspecified
Version:	44	CC:	amatej, jonathan, mcatanza, pkratoch, ppisar, rpm-software-management
Target Milestone:	---	Flags:	fedora-admin-xmlrpc: mirror+
Target Release:	---
Hardware:	x86_64
OS:	Linux
Whiteboard:
Fixed In Version:		Doc Type:	---
Doc Text:		Story Points:	---
Clone Of:		Environment:
Last Closed:	2026-09-08 10:13:32 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 tor 2026-08-30 19:26:39 UTC

Running Fedora 44 Gnome 50 I've had an issue that I was prompted (via checkbox) to "Install pending software updates" that has persisted despite numerous restarts into offline transactions. While troubleshooting this it led me to an issue regarding dnf and the GsDnf5-plugin

What I found:
- dnf update found no outstanding packages to update
- There were nothing in PackageKit explaining the "missing updates"
- pkcon refresh force and get-updates found nothing
- I stopped the gnome-software user service and restarted with --verbose to see what was happening:
09:41:24:049 GsDnf5 Creating new session
09:41:24:087 Gs  running GetOfflineUpdateState job, elapsed time since creation 37ms
- Exploring the /var/lib/dnf folder i found the ./offline folder, with a subfolder packages filed with rpms from the last week. 
- Testing some installed versions against the rpms I found that they all matched - rpm version == installed version.
- running dnf offline status it returned a message containing “The system has been modified since the offline transaction was prepared.”
- running dnf offline clean caused all of the rpms (indeed the entire /var/lib/dnf/offline folder) to be deleted
- This resolved the issue with the persisting "Install pending software updates"

Probable cause:
- gnome-softwares automatic install of new software (or is it dnf-automatic ?) schedules an offline update.
- This causes rpms to be downloaded to /var/lib/dnf/offline for offline install
- Before rebooting I instead manually ran dnf update, to update my systemThe rpms in /var/lib/dnf/offline were however NOT cleaned, but left in place. See https://github.com/rpm-software-management/dnf5/issues/2831
- On entering "offline install" mode installing the packages probably then failed the install as all the rpm were already installed, this did however NOT lead to them being cleaned up
- After logging in to fedora anew gnome-software still thinks there are uninstalled updates
- The "Install pending software updates" checkbox persists...

Possible fix?
I am not familiar with your codebase, nor with how GsDnf5 determines if there are pending updates, but based on the behaviour above it seems to check /var/lib/dnf/offline. This will give a false positive when dnf does not clean up the offline packages when user does a manual dnf update. Maybe either checking dnf offline status and if it gives a warning about "system changes" calling dnf offline clean before proceeding with checking for pending updates?The problem will probably reoccur and will make sure to dump everything to logs then to share in this issue.

PS: I tried posting this to the gnome-software gitlab project, but was told that this issue is upstream and to file the issue here at bugzilla.redhat.com

Reproducible: Sometimes

Steps to Reproduce:
1.Wait for automatic updates to notify you that there are pending/available updates
2.Instead of installing during Shutdown via "Install pending software updates" instead run dnf update manually
Actual Results:
See a persistent "Install pending software updates" in the Shutdown/Reboot dialog despite there being no updates to install

Expected Results:
Manual install of packages via dnf update should clear those packages from being marked as "Pending software updates", removing the checkbox from the Shutdown/Reboot dialogs

Comment 1 amatej 2026-08-31 11:00:03 UTC

I think should be fixed by https://github.com/rpm-software-management/dnf5/pull/2736 can you still reproduce it with dnf5 >= 5.4.3.0? It was released to Fedoras only about a week ago.

Comment 2 tor 2026-09-04 10:54:51 UTC

I will check next time the situation with "Install pending software updates" arises again. Checked my version and I'm on 5.4.3.0 as of now.

Will return and post here then!

Comment 3 tor 2026-09-07 10:35:33 UTC

Still an issue on dnf 5.4.3.0:
```
╰─❮ dnf --version
dnf5 version 5.4.3.0
dnf5 plugin API version 2.0
libdnf5 version 5.4.3.0
libdnf5 plugin API version 2.2

Loaded dnf5 plugins:
  name: builddep
  version: 1.0.0
  API version: 2.0

  name: changelog
  version: 1.0.0
  API version: 2.0

  name: config-manager
  version: 0.1.0
  API version: 2.0

  name: copr
  version: 0.1.0
  API version: 2.0

  name: needs_restarting
  version: 1.0.0
  API version: 2.0

  name: repoclosure
  version: 1.0.0
  API version: 2.0

  name: repomanage
  version: 1.0.0
  API version: 2.0

  name: reposync
  version: 1.0.0
  API version: 2.0

Loaded libdnf5 plugins:
  name: appstream
  version: 1.0.0
  API version: 2.0

  name: expired-pgp-keys
  version: 1.0.0
  API version: 2.1
```

I waited until I got a GNOME notification that updates need to be installed. Immediately ran:
```
╰─❮ sudo dnf offline status
[sudo] password for torep:
The system has been modified since the offline transaction was prepared. The offline transaction initiated by the following command is no longer valid:
  dnf5daemon-server
To reschedule, run the command above. To clean up, run `dnf5 offline clean`.
```
I ran shutdown with the "Install pending software updates" checked TWICE, it did not appear that anything happened in "offline transaction"-mode. 
1) dnf offline status gives the exact same output
2) There are rpms pending in /var/lib/dnf/offline/packages matches the packages listed by running dnf update (did not yet run this)
```
╭─  /var/lib/dnf/offline/packages                                                                           12:25:50
╰─❮ ll
.rw-r--r--@ 136M root root  7 Sep 11:53 chromium-152.0.7977.82-1.fc44.x86_64.rpm
.rw-r--r--@  15M root root  7 Sep 11:53 chromium-common-152.0.7977.82-1.fc44.x86_64.rpm
.rw-r--r--@ 183M root root  7 Sep 11:54 claude-desktop-unofficial-1.46388.2-3.2.4-1.x86_64.rpm
.rw-r--r--@ 3.1M root root  7 Sep 11:53 gegl04-0.4.70-5.fc44.x86_64.rpm
.rw-r--r--@  28k root root  7 Sep 11:53 gegl04-matting-levin-0.4.70-5.fc44.x86_64.rpm
.rw-r--r--@ 200M root root  7 Sep 11:53 joplin-3.7.16-1.rp.fc44.taw.x86_64.rpm
.rw-r--r--@ 104k root root  7 Sep 11:53 librepo-1.21.0-2.fc44.x86_64.rpm
.rw-r--r--@ 121k root root  7 Sep 11:53 libwmf-0.2.16-1.fc44.x86_64.rpm
.rw-r--r--@  79k root root  7 Sep 11:53 libwmf-lite-0.2.16-1.fc44.x86_64.rpm
╰─❮ sudo dnf update
Updating and loading repositories:
Repositories loaded.
Package                                Arch   Version                             Repository                        Size
Upgrading:
 chromium                              x86_64 0:152.0.7977.82-1.fc44              updates                      345.3 MiB
   replacing chromium                  x86_64 0:152.0.7977.75-1.fc44              updates                      345.3 MiB
 chromium-common                       x86_64 0:152.0.7977.82-1.fc44              updates                       65.5 MiB
   replacing chromium-common           x86_64 0:152.0.7977.75-1.fc44              updates                       65.5 MiB
 claude-desktop-unofficial             x86_64 0:1.46388.2-3.2.4.fc42              claude-desktop-unofficial    583.0 MiB
   replacing claude-desktop-unofficial x86_64 0:1.40609.1-3.2.3.fc42              claude-desktop-unofficial    574.2 MiB
 gegl04                                x86_64 0:0.4.70-5.fc44                     updates                       13.8 MiB
   replacing gegl04                    x86_64 0:0.4.70-2.fc44                     fedora                        13.8 MiB
 gegl04-matting-levin                  x86_64 0:0.4.70-5.fc44                     updates                       39.4 KiB
   replacing gegl04-matting-levin      x86_64 0:0.4.70-2.fc44                     fedora                        39.4 KiB
 joplin                                x86_64 0:3.7.16-1.rp.fc44.taw              copr:copr.fedorainfracloud.o 196.5 MiB
   replacing joplin                    x86_64 0:3.6.16-1.rp.fc44.taw              copr:copr.fedorainfracloud.o 156.9 MiB
 librepo                               x86_64 0:1.21.0-2.fc44                     updates                      253.1 KiB
   replacing librepo                   x86_64 0:1.21.0-1.fc44                     updates                      253.1 KiB
 libwmf                                x86_64 0:0.2.16-1.fc44                     updates                      420.7 KiB
   replacing libwmf                    x86_64 0:0.2.13-9.fc44                     fedora                       420.7 KiB
 libwmf-lite                           x86_64 0:0.2.16-1.fc44                     updates                      167.9 KiB
   replacing libwmf-lite               x86_64 0:0.2.13-9.fc44                     19278be6a81040f5b6cbc7bacea5 159.4 KiB
```
3) Now I run dnf update and confirm. Output ends with:
```
Warning: Pending offline transaction has been invalidated.
To reschedule, run: dnf5daemon-server
Complete!
```
4) Running dnf offline status it is NOT reset:
```
╰─❮ sudo dnf offline status
The system has been modified since the offline transaction was prepared. The offline transaction initiated by the following command is no longer valid:
  dnf5daemon-server
To reschedule, run the command above. To clean up, run `dnf5 offline clean`.
```
5) The "Install pending software updates" is still there...

Comment 4 tor 2026-09-07 11:01:20 UTC

6) Rebooting with "Install..." checked again takes me to "offline transaction"-mode where nothing appears to happen
7) On rebooting the "Install..." checkbox is still there and dnf offline status shows the exact same output:
```
╰─❮ sudo dnf offline status
[sudo] password for torep:
The system has been modified since the offline transaction was prepared. The offline transaction initiated by the following command is no longer valid:
  dnf5daemon-server
To reschedule, run the command above. To clean up, run `dnf5 offline clean`.
```

A side-observation that may (or may not?) be insignificant is that when I run the Shutdown option with the "Install..." box checked it does not turn off the machine, rather it just restarts it.

Comment 5 Michael Catanzaro 2026-09-07 22:15:53 UTC

Note that PackageKit is not used at all anymore since Fedora 44.

Comment 6 Petr Pisar 2026-09-08 10:13:32 UTC


*** This bug has been marked as a duplicate of bug 2529146 ***