How to consolidate repositories to be used by DNF and Software app

I run Fedora 42 with Gnome 48.
I used to update my installation for years with the command:

dnf update --best --allowerasing

Now I detected that Fedora’s Software App seem to use different repositories and marks some software to be updated that are not covered with my

dnf update --best --allowerasing

How can I assure that the Software app does not use different repositories? How can I assure that my dnf command covers all software that is installed?

Besides my questions: I know that dnf was recently replaced by dnf5 and that I now should use

dnf5 upgrade --best --allowerasing

Thank you in advance
Jochen

Related “Common Issues” page:

Thank you, but I checked that linked common issue before posting my question. Unfortunately that coomon issue does not match with my environment.

Let me be more precise.
My /etc/dnf/repos.override.d is empty.
My /etc/yum.repos.d contains 14 entries. They are all listed when I execute

[15:00:24]\jojo@waldstadion:~$ dnf5 repo list
repo id                                                                       repo name                                                                                      
brave-browser                                                                 Brave Browser                                                                                  
CollaboraOnline                                                               CollaboraOnline                                                                                
copr:copr.fedorainfracloud.org:phracek:PyCharm                                Copr repo for PyCharm owned by phracek                                                         
fedora                                                                        Fedora 42 - x86_64                                                                             
fedora-cisco-openh264                                                         Fedora 42 openh264 (From Cisco) - x86_64                                                       
google-chrome                                                                 google-chrome                                                                                  
rpmfusion-free                                                                RPM Fusion for Fedora 42 - Free                                                                
rpmfusion-free-tainted                                                        RPM Fusion for Fedora 42 - Free tainted                                                        
rpmfusion-free-updates                                                        RPM Fusion for Fedora 42 - Free - Updates                                                      
rpmfusion-nonfree                                                             RPM Fusion for Fedora 42 - Nonfree                                                             
rpmfusion-nonfree-nvidia-driver                                               RPM Fusion for Fedora 42 - Nonfree - NVIDIA Driver                                             
rpmfusion-nonfree-steam                                                       RPM Fusion for Fedora 42 - Nonfree - Steam                                                     
rpmfusion-nonfree-updates                                                     RPM Fusion for Fedora 42 - Nonfree - Updates                                                   
updates                                                                       Fedora 42 - x86_64 - Updates   

Whereas the additional Software repos are:

The updates that Software actually offers are:

although I executed sudo dnf5 upgrade --best --allowerasing just minutes before. That’s why I am searching where Software manages its repositories and ask how I can consolidate with DNF5.
I hope my concerns are clearer now.

That makes it clearer. So the GNOME Software app there is consolidating updates from three different types of source:

  1. Repos that provide packages in .rpm format. From the command line, you indeed use dnf to update these.
  2. Repos that provide packages as flatpaks. From the command line, you use flatpak update to update these.
  3. Manufacturer firmware updates. From the command line, you use fwupdmgr for these.

As far as I know, there isn’t a plan to expand the scope of dnf to include Flatpak and firmware updates.

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To get the absolute latest updates, you also need --refresh option for the dnf command. By the way, currently dnf and dnf5 are the exact same program.

Thank you for the hints.
I know that dnf is still an alias for dnf5, but sometimes the commands change, e.g. instead of dnf update it is now dnf upgrade.

Hey,

I’m going to speculate that what you are really asking for is how to use the flatpak cli command to update all the flatpaks on the system in a similar way that you are using dnf cli command to update the rpms. Assuming that’s true you’d want to learn how to use the flatpak command starting probably with flatpak update

But if my guess is what you are looking for is wrong, then there is probably a deeper confusion about how things work that needs to be addressed.

There are two different packaging technologies in play here… rpm and flatpaks

rpms is much more granular in practise than flatpaks… which is a direct result of the design and intent of each packaging system. rpms packages are meant to be deeply interconnected via a set of shared dependencies, down to the individual versioned library level. rpms are a system oriented packaging concept. flatpaks packages are application oriented packaging concept and are intended to be far less granular and far less interconnected via dependencies, where applications are encourage to bundle libraries they need instead using the systemwide (or use one of a few curated runtimes that bundle a lot of common libraries).

dnf cli command only manages rpm packages and rpm repositories

the flatpak cli command only manages flatpak packages and flatpak repos

The gnome software ui provides an overlay user interface that sort of abstracts multiple packaging systems, for common operations, but does not expose all the functionality of any packaging system.

There’s no way to “consolidate” rpm and flatpak based packaging in any real sense afaik.
At best you can use the systemwide rpm update tools and the flatpak update tools on the same cadence.

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In dnf4 dnf update was an deprecated alias for dnf upgrade. From man dnf4

   Upgrade Command
       Command: upgrade
       Aliases: up
       Deprecated aliases: update, upgrade-to, update-to, localupdate

In dnf5 this is still the case, so you can use dnf5 update or dnf5 upgrade.

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You can make a bash alias for the upgrade commands:

$ mkdir -p ~/.bashrc.d/
$ echo "alias updateos='sudo dnf upgrade --refresh -y && flatpak update -y && fwupdmgr refresh && fwupdmgr update'" | tee -a ~/.bashrc.d/aliases >/dev/null
$ source ~/.bashrc.d/aliases

Then run updateos from CLI whenever you want to update the system.

You can remove the -y (i.e. --assumeyes) flag for greater control of the update process (but slightly less automated), as well as change the name of the alias to your liking.

Dear all,

thank you all for you explanations, hints and suggestions. With your help this issue is fixed for me.

best regards
Jochen

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