Flatpaks Won't Run after Fedora 43 Upgrade

1

I upgraded to F43 using DNF System Plugin. After which some of my previously installed flatpaks will not run with the error:

bwrap: Can't mkdir parents for /home/rkroeker/.var/app/${app-name}/config/user-dirs.dirs: No such file or directory

(where ${app-name} is replaced with the literal application name). Unfortunately I didn’t check what versions of the runtime existed before the upgrade. I’m running 1.16.1 right now.

They are ‘system’ installed (vs user) and I’ve attempted to reinstall them both at system and user scope. What are my next steps here?

2

Did you figure this out? I didn’t get this problem after upgrading to Fedora 43 through Gnome Software, but I have two things you could try looking at:

  1. Fedora 43 (actually throughout RHEL) dropped x11 support. If an app was written for x11 and does not work with xWayland, it won’t work. For me, my manual install of the minecraft launcher stopped working on both Fedora 43 computers. (Ironically considering the topic, my solution was to switch to flatpaked minecraft launchers.) Still, you could check if the flatpaks you are having trouble with have only –socket=x11 or if they have –socket=waylandYou can check this in the manifest or with flatseal. If the flatpak only has x11 socket access, perhaps that is the problem?
  2. Last I checked the default flatpak source for Fedora is not Flathub. Fedora makes its own flatpaks, and enables their own repository by default while disabling Flathub. Go into your software sources and make sure that Flathub is enabled. Even if you used terminal to install your flatpaks from flathub, the system will not automatically update them unless you manually enable the Flathub repository. Otherwise, you must run flatpak update in terminal to update any flatpaks from Flathub.
3

I did not figure it out. After a number of re-install attempts and removing the directory roots I rolled back to Fedora 42.

I can setup a VM in which I can likely test this. I looked around for more advanced troubleshooting / debugging techniques, but couldn’t find the underlying root cause.

4

Can you name the apps, that stopped working?