Hello Fedora community,
I’m running Fedora 42 with KDE Plasma, and I’m seeing a package-conflict error in Discover every time I try to apply updates. I’m not sure how to proceed and would appreciate any advice.
I opened Discover to apply system updates. Discover keeps reporting different versions of the same conflict:
I’ve tried restarting discover and running sudo dnf upgrade from the terminal. Despite this, the GUI update still fails, and I’m uncertain which package I should remove or how to resolve the duplication.
Any guidance on next steps would be very much appreciated.
I was expecting to see in the output of dnf list also the package from the updates repo. It’s possible that some repos (specifically updates) are disabled. What is the output of dnf repolist?
The --refresh flag of dnf should have presented the fedora and updates repos, which even though seem to be enabled, are not sent to the output. For the same reason the package NetworkManager-vpnc with version1.4.0-3.fc42 is not found by the command.
Is there anything relevant about your system, that might cause this outcome? Upgrade from a previous release, tweaks of the dnf repos etc.
Or maybe an issue with the mirrors?
What is the output of dnf5 repolist --all and dnf5 repo info updates?
EDIT: What about dnf4 config-manager --dump-variables?
The output for dnf5 repolist --all is a bit big. But here’s the output for dnf5 repo into updates and dnf4 config-manager --dump-variables.
❯ dnf5 repo info updates
Updating and loading repositories:
Repositories loaded.
Repo ID : updates
Name : updates
Status : enabled
Priority : 5
Cost : 1000
Type : available
Metadata expire : 21600 seconds (last: unknown)
Skip if unavailable : true
Config file : /etc/dnf/dnf.conf
URLs :
OpenPGP :
Verify repodata : false
Verify packages : true
Repodata info :
Available packages : 0
Total packages : 0
Size : 0.0 B
Revision :
Updated : 1970-01-01 00:00:00
❯ dnf4 config-manager --dump-variables
Invalid configuration value: installonly_limit=1 in /etc/dnf/dnf.conf; value 1 is not allowed
Repository 'updates' is missing name in configuration, using id.
Repository 'fedora' is missing name in configuration, using id.
Repository fedora is listed more than once in the configuration
Repository updates is listed more than once in the configuration
arch = x86_64
basearch = x86_64
releasever = 42
releasever_major = 42
releasever_minor =
The dnf repo info updates, as well as the last command show that the fedora and updates repos are wrong.
The updates repo certainly should not point to the /etc/dnf/dnf.conf file. Do you remember tweaking your system around this issue?
The dnf repo info updates should have an output similar to this one:
$ dnf repo info updates
Updating and loading repositories:
Repositories loaded.
Repo ID : updates
Name : Fedora 42 - aarch64 - Updates
Status : enabled
Priority : 99
Cost : 1000
Type : available
Metadata expire : 21600 seconds (last: 2025-05-15 13:13:57)
Skip if unavailable : false
Config file : /etc/yum.repos.d/fedora-updates.repo
URLs :
Base URL : https://mirror.group.one/fedora/updates/42/Everything/aarch64/ (73 more)
Metalink : https://mirrors.fedoraproject.org/metalink?repo=updates-released-f42&arch=aarch64
OpenPGP :
Keys : file:///etc/pki/rpm-gpg/RPM-GPG-KEY-fedora-42-aarch64
Verify repodata : false
Verify packages : true
Repodata info :
Available packages : 9604
Total packages : 9604
Size : 24.8 GiB
Revision : 1747268953
Updated : 2025-05-15 01:47:19
Notice that the Config file variable points to the correct repo file.
Your system currently has no reference to the packages from the fedora and updates repos. If you could remember what actions did change these settings, there might be an easier fix available.
