Error: No such ref 'runtime/org.fedoraproject.Platform/x86_64/f39' in remote fedora

I’m running a Silverblue F41 installation. flatpak update gives me various messages such as:

Info: runtime org.freedesktop.Platform.GL.default branch 22.08-extra is end-of-life, with reason:
   org.freedesktop.Platform 22.08 is no longer receiving fixes and security updates. Please update to a supported runtime version.
Info: applications using this extension:
   com.google.Chrome, com.microsoft.EdgeDev, com.belmoussaoui.Obfuscate, com.raggesilver.BlackBox, com.ranfdev.Geopard, net.fasterland.converseen

…before finishing with:

error: No such ref 'runtime/org.fedoraproject.Platform/x86_64/f39' in remote fedora

I’m noticing that there don’t appear to be many application updates available (Signal can no longer be used or updates), which I presume is related.

flatpak remotes says:

Name          Options
fedora        system
flathub       system
flathub       user
gnome-nightly user

The f39 runtime is not pinned. There was also a pinned f38 runtime, which I unpinned and uninstalled as it was unused.

How should I proceed here? If i try uninstalling the f39 runtime then various apps will be uninstalled with it.

You’ve obviously upgraded/rebased from previous Fedora atomic versions.

Can you post the output of:

  • flatpak list -- runtime
  • flatpak pin
  • flatpak list --app --columns=application,origin,runtime | grep -E 'org.freedesktop.Platform.GL.default' | grep -E '22.08'
  • flatpak list --app --columns=application,origin,runtime | grep -E 'org.fedoraproject.Platform' | grep -E 'f39'?

Indeed I have! I’m not sure whether I did so correctly, though…
Anyway, answers below:

% flatpak list --runtime    
Name                        Application ID                         Version                  Branch      Origin        Installation
peazip i386 addon           io.github.peazip.PeaZip.Addon.i386     1.0.0                    stable      flathub       system
Codecs                      org.chromium.Chromium.Codecs                                    stable      flathub       system
Fedora Platform             org.fedoraproject.Platform             39                       f39         fedora        system
Freedesktop Platform        org.freedesktop.Platform               21.08.22                 21.08       flathub       system
Freedesktop Platform        org.freedesktop.Platform               22.08.25                 22.08       flathub       system
Freedesktop Platform        org.freedesktop.Platform               freedesktop-sdk-23.08.27 23.08       flathub       system
Freedesktop Platform        org.freedesktop.Platform               freedesktop-sdk-24.08.5  24.08       flathub       system
i386                        org.freedesktop.Platform.Compat.i386                            23.08       flathub       system
Mesa                        org.freedesktop.Platform.GL.default    21.3.9                   21.08       flathub       system
Mesa                        org.freedesktop.Platform.GL.default    24.0.7                   22.08       flathub       system
Mesa (Extra)                org.freedesktop.Platform.GL.default    24.0.7                   22.08-extra flathub       system
Mesa                        org.freedesktop.Platform.GL.default    24.3.1                   23.08       flathub       system
Mesa (Extra)                org.freedesktop.Platform.GL.default    24.3.1                   23.08-extra flathub       system
Mesa                        org.freedesktop.Platform.GL.default    24.2.5                   24.08       flathub       system
Mesa                        org.freedesktop.Platform.GL.default    24.3.1                   24.08       gnome-nightly user
Mesa (Extra)                org.freedesktop.Platform.GL.default    24.2.5                   24.08extra  flathub       system
Mesa (Extra)                org.freedesktop.Platform.GL.default    24.3.1                   24.08extra  gnome-nightly user
Mesa                        org.freedesktop.Platform.GL32.default  24.0.2                   23.08       flathub       system
Mesa (Extra)                org.freedesktop.Platform.GL32.default  24.0.2                   23.08-extra flathub       system
openh264                    org.freedesktop.Platform.openh264      2.1.0                    2.0         flathub       system
openh264                    org.freedesktop.Platform.openh264      2.1.0                    2.2.0       flathub       system
openh264                    org.freedesktop.Platform.openh264      2.4.1                    2.4.1       flathub       system
openh264                    org.freedesktop.Platform.openh264      2.4.1                    2.4.1       flathub       user
openh264                    org.freedesktop.Platform.openh264                               2.4.1beta   gnome-nightly user
openh264                    org.freedesktop.Platform.openh264      2.5.0                    2.5.0beta   gnome-nightly user
Freedesktop SDK             org.freedesktop.Sdk                    22.08.21                 22.08       flathub       system
GNOME Application Platform… org.gnome.Platform                                              44          flathub       system
GNOME Application Platform… org.gnome.Platform                                              45          flathub       system
GNOME Application Platform… org.gnome.Platform                                              46          flathub       system
GNOME Application Platform… org.gnome.Platform                                              master      gnome-nightly user
adw-gtk3-dark Gtk Theme     org.gtk.Gtk3theme.adw-gtk3-dark                                 3.22        flathub       user
Adwaita theme               org.kde.KStyle.Adwaita                                          5.15-22.08  flathub       system
Adwaita theme               org.kde.KStyle.Adwaita                                          5.15-23.08  flathub       system
Adwaita theme               org.kde.KStyle.Adwaita                                          6.8         flathub       user
KDE Application Platform    org.kde.Platform                                                5.15-22.08  flathub       system
KDE Application Platform    org.kde.Platform                                                5.15-23.08  flathub       system
KDE Application Platform    org.kde.Platform                                                6.8         flathub       user
QGnomePlatform              org.kde.PlatformTheme.QGnomePlatform                            5.15-22.08  flathub       system
QGnomePlatform              org.kde.PlatformTheme.QGnomePlatform                            5.15-23.08  flathub       system
QAdwaitaDecorations         …WaylandDecoration.QAdwaitaDecorations                          5.15-22.08  flathub       system
QAdwaitaDecorations         …WaylandDecoration.QAdwaitaDecorations                          5.15-23.08  flathub       system
QGnomePlatform-decoration   …dDecoration.QGnomePlatform-decoration                          5.15-22.08  flathub       system
QGnomePlatform-decoration   …dDecoration.QGnomePlatform-decoration                          5.15-23.08  flathub       system
% flatpak pin
No pinned patterns
% flatpak list --app --columns=application,origin,runtime | grep  -E 'org.freedesktop.Platform.GL.default' | grep -E '22.08'
%
% flatpak list --app --columns=application,origin,runtime | grep  -E 'org.fedoraproject.Platform' | grep -E 'f39'
ca.desrt.dconf-editor	fedora	org.fedoraproject.Platform/x86_64/f39
com.github.tchx84.Flatseal	fedora	org.fedoraproject.Platform/x86_64/f39
com.transmissionbt.Transmission	fedora	org.fedoraproject.Platform/x86_64/f39
org.audacityteam.Audacity	fedora	org.fedoraproject.Platform/x86_64/f39
org.fedoraproject.MediaWriter	fedora	org.fedoraproject.Platform/x86_64/f39
org.gimp.GIMP	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.Calculator	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.Calendar	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.Characters	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.Cheese	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.Connections	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.Contacts	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.Evince	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.Extensions	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.Logs	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.Maps	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.NautilusPreviewer	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.SoundJuicer	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.TextEditor	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.Weather	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.baobab	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.clocks	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.eog	fedora	org.fedoraproject.Platform/x86_64/f39
org.gnome.font-viewer	fedora	org.fedoraproject.Platform/x86_64/f39
org.remmina.Remmina	fedora	org.fedoraproject.Platform/x86_64/f39

Thanks!

A couple of things to notice:

1.
Silverblue ships most of the GNOME apps by default as Flatpaks. I am not sure if it is a missing feature of the system upgrades on Fedora atomic systems or not, but these default Flatpak apps seem to have stayed on their F39 versions. I have missed to ask for the column version in the last command, but I assume their version is not 47.*.

You can check if after installing runtime org.fedoraproject.Platform branch f41, would a flatpak udpate command also bring these apps from the fedora remote to their 47 version. If not, you might need to manually remove and reinstall them.

2.
I wonder if the above issue is caused by missing Flatpak pins. Normally the runtime org.fedoraproject.Platform corresponding to the version of the base system, so f41 in our case, should be pinned. After installing it, you might want to pin it[1].

I haven’t upgraded/rebased my Silverblue F41 system, so I wonder if this is taking place now automatically, or it is expected that the user takes care of it manually. If the latter is true, we’d have to ask the Docs Team for updating the guide accordingly.

3.
You have the same branches of the same runtimes (but on different versions) from 2 different remotes: flathub and gnome-nightly. I am not sure if this is a working setup, or if it’s the cause of some of the issues you’re experiencing. If not necessary, you could remove the gnome-nightly remote.

4.
Try removing unused runtimes with flatpak uninstall --unused.


  1. For as long as you’re on the same version of the base install, ↩︎

1 Like

I’ve been encountering this when trying to install the f41 runtime:

% F: An error was encountered searching remote ‘fedora’ for ‘org.fedoraproject.Platform/f41’: Unable to load summary from remote fedora: GPG verification enabled, but no summary found (check that the configured URL in remote config is correct)
error: No remote refs found for ‘org.fedoraproject.Platform/f41’

Where would that remote URL be specified? The software app shows that registry.fedoraproject.org is enabled.

Do you have a similar output[1]:

$ flatpak install org.fedoraproject.Platform
Looking for matches…
Similar refs found for ‘org.fedoraproject.Platform’ in remote ‘fedora’ (system):

   1) runtime/org.fedoraproject.Platform/aarch64/f40
   2) runtime/org.fedoraproject.Platform/aarch64/f41
   3) runtime/org.fedoraproject.Platform/aarch64/f35
   4) runtime/org.fedoraproject.Platform/aarch64/f36
   5) runtime/org.fedoraproject.Platform/aarch64/f37
   6) runtime/org.fedoraproject.Platform/aarch64/f38
   7) runtime/org.fedoraproject.Platform/aarch64/f39

Which do you want to use (0 to abort)? [0-7]:

  1. Except for the different architecture, obviously. ↩︎

No, I get the error mentioned above, i.e. GPG verification enabled but no summary found.

flatpak repair of any help?

Unfortunately not. I tried that before and it does this:

Working on the system installation at /var/lib/flatpak
[213/213] Verifying flathub:runtime/org.libreoffice.LibreOffice.Locale/x86_64/stable…
Checking remotes...

Here’s the config file I found; looks OK to me…

% cat /var/lib/flatpak/repo/config
[core]
repo_version=1
mode=bare-user-only
min-free-space-size=500MB
xa.pinned=

[remote "flathub"]
url=https://dl.flathub.org/repo/
xa.title=Flathub
gpg-verify=true
gpg-verify-summary=true
xa.comment=Central repository of Flatpak applications
xa.description=Central repository of Flatpak applications
xa.icon=https://dl.flathub.org/repo/logo.svg
xa.homepage=https://flathub.org/
xa.title-is-set=true
xa.comment-is-set=true
xa.description-is-set=true
xa.disable=false

[remote "fedora-testing"]
url=oci+https://registry.fedoraproject.org#testing
xa.title=Fedora Flatpaks (testing)
xa.title-is-set=true
xa.disable=true

[remote "fedora"]
gpg-verify=true
gpg-verify-summary=true
url=https://registry.fedoraproject.org
url-is-set=true

I will check the config on my system later, I am not near a Fedora system at the moment.

  1. You probably have too many flatpak remotes. I only use system remotes, they save space when using multiple users and need privileges to manage
  2. You may want to remove the fedora remote. It is nice and all, but not official and misses the media codecs, so you will use flathub anyways
  3. No idea if all those apps are just outdated, happens quite often.
  4. Just try and remove all remotes and add them back?

First remove all software you dont need. This includes runtimes if you dont actually use the software.

flatpak remote-delete --force flathub
flatpak remote-delete --force fedora
flatpak remote-delete --force flathub --user
flatpak remote-delete --force gnome-nightly --user

–force does not remove the apps. So you may want not to use that and swap the apps with flathub apps instead.

You want to avoid for sure to have outdated apps with no repo.

flatpak remove does not delete app data. So you might want to write down your installed apps, remove all repos, add flathub and gnome-nightly and install them app.

This is the config of my fedora repo:

$ cat /var/lib/flatpak/repo/config 
# [...]
[remote "fedora"]
url=oci+https://registry.fedoraproject.org
gpg-verify=true
gpg-verify-summary=true
# [...]

You might want to adjust yours accordingly and check afterwards if the errors still occur (e.g. when trying to install the org.fedoraproject.Platform runtime.

Yes, that’s the problem. The Fedora remote uses OCI, so it needs to be specified that way. But don’t edit the file manually, use flatpak remote-modify:

flatpak remote-modify fedora --url=oci+https://registry.fedoraproject.org

I really can’t imagine how this would have happened.

1 Like

Thanks, the OCI URL modification did the trick; I’m now watching 120 Flatpaks update.
I’m not sure either what happened here. I’ve upgraded this system from earlier releases (starting on 39, perhaps) but don’t recall anything unusual happening.

1 Like

I thought the Fedora Flatpak was the official one. Did i miss something? I tried to remove it and replace it with flathub apps a few weeks ago, by issuing:

flatpak install --reinstall flathub $(flatpak list --app-runtime=org.fedoraproject.Platform --columns=application | tail -n +1 )

and removing the remote afterwards. Unfortunately, some applications didn’t work properly after that, for example I had problems with the file preview integration in Nautilus. So I went back to the default Fedora Flathub for all pre-installed Gnome applications. So I wouldn’t recommend this step.

Fedora Flatpaks are official by Fedora. They are not maintained by the developers of the applications.

Honestly I dont get why that remote exists.

I dont know about baobab, it should work from Flathub but no idea.

For sure Fedora Flatpak apps may work well, sometimes better, often worse. Absolutely though they add additional complexity to the system which isnt really needed.

Is your problem resolved after removing all apps and remotes and reinstalling them?