Flatpaks Do Not Open

I will try to provide as much information as I can, and if more is needed please ask. Flatpaks struggle to open in a lot of cases for me, and part of it I think has to do with permissions, but I can only guess based on what I have tried so far. What usually happens is that I click launch, the application will visibly be opening on my task bar for a few moments, then disappear as if it closed for some odd reason.

I have done the following:

  1. flatpak update
  2. flatpak repair
  3. Changing around permissions in flatseal
  4. Opening the application in the terminal first without sudo, and then with sudo

None of these worked. The closest I have gotten it to work is that opening up an application with sudo in the terminal - in this case the Hytale launcher - will indeed open up the window, but as an example it can’t launch the browser to sign in, and it closes itself soon after.

I sincerely hope I can get some help here. Don’t know if I’m the one that borked my own system here but I would very much like to use flatpaks lol. I’m not tech illiterate but I would also appreciate if certain fixes could be explained in a way that’s accessible to newbies. Thank you.

I would completely remove Flatpak and reinstall it.

flatpak uninstall --all and then check for any remaining files: flatpak repair (to make sure everything is gone). Then reinstall. Yes, it’s annoying, but it’s the better solution (in my opinion).

I followed your instructions, did a fresh install of flatpak too, did not work. Issue persists unfortunately.

With KDE 40, the kernel modules or X11 drivers might be older, which could lead to conflicts with newer Flatpaks. Perhaps it would be better to switch to a newer Fedora version? But that’s just a guess… Maybe check which Flatpak version you’re using with flatpak --version. Versions below 1.10.x might cause problems if you’re using apps that require maximum graphics acceleration. But as I said, these are just guesses.

I’ll provide some info here:
I am using Fedora 43, my flatpak version is 1.16.2, and everything else is up to date.

Does:
flatpak run --verbose --command=sh flatpak-application-id
and then running the flatpak show any obvious errors.
e.g.
flatpak run --verbose --command=sh com.github.tchx84.Flatseal
com.github.tchx84.Flatseal

Tried this with two applications I know have issues, both end with that bwrap line. I know nothing about that or how I would fix that, any info there would be appreciated.

Can you check:
mount | grep -E '\/home|\/var'

and see if something is mounted with noexec

I get this.

Which ones are broken?

Just above the lines about bwrap I see a failed attempt to use pulseaudio.
Pulseaudio has not been used on fedora for several release versions so that may be related to the failure.
Do you happen to have the pipewire-pulseaudio package installed or not? That package is supposed to allow most apps depending upon pulseaudio to work with pipewire.

Sorry I’m sort of out of my depth here, are you asking which applications are broken?

I do have that package, yes.

Which flatpak apps don’t run?

Seems to me like they are mostly games. Flatseal, for example, will launch just fine. Games like Vintage Story, Hytale, PokeMMO, etc. have trouble. However, Obsidian also has this issue.

Can you post
flatpak list
as pre-formated text </>

You could try resetting permissions completely for one of the apps in question
e.g. flatpak override --reset io.mrarm.mcpelauncher
or latpak override --reset --user io.mrarm.mcpelauncher
if you’re running a user installation.

You can also do this in flatseal by hitting the reset button after selecting an app, last I looked it was at the top right.

You could also try cleaning up unused runtimes.
flatpak remove --unused

1 Like
Name                                           Application ID                                         Version                          Branch              Origin                        Installation
Vintage Story                                  at.vintagestory.VintageStory                           1.21.6                           stable              flathub                       system
Hytale Launcher                                com.hypixel.HytaleLauncher                                                              master              hytalelauncher-origin         system
PokeMMO                                        com.pokemmo.PokeMMO                                    3.0f                             stable              flathub                       system
Minecraft Bedrock Launcher                     io.mrarm.mcpelauncher                                  v1.6.0                           stable              flathub                       system
Obsidian                                       md.obsidian.Obsidian                                   1.11.4                           stable              flathub                       system
Freedesktop Platform                           org.freedesktop.Platform                               freedesktop-sdk-24.08.28         24.08               flathub                       system
Freedesktop Platform                           org.freedesktop.Platform                               freedesktop-sdk-25.08.6          25.08               flathub                       system
Mesa                                           org.freedesktop.Platform.GL.default                    25.2.6                           24.08               flathub                       system
Mesa (Extra)                                   org.freedesktop.Platform.GL.default                    25.2.6                           24.08extra          flathub                       system
Mesa                                           org.freedesktop.Platform.GL.default                    25.2.6                           25.08               flathub                       system
Mesa (Extra)                                   org.freedesktop.Platform.GL.default                    25.2.6                           25.08-extra         flathub                       system
nvidia-580-119-02                              org.freedesktop.Platform.GL.nvidia-580-119-02                                           1.4                 flathub                       system
Nvidia VAAPI driver                            org.freedesktop.Platform.VAAPI.nvidia                                                   25.08               flathub                       system
Codecs Extra Extension                         org.freedesktop.Platform.codecs-extra                                                   25.08-extra         flathub                       system
openh264                                       org.freedesktop.Platform.openh264                      2.5.1                            2.5.1               flathub                       system
GNOME Application Platform version 48          org.gnome.Platform                                                                      48                  flathub                       system
GNOME Application Platform version 49          org.gnome.Platform                                                                      49                  flathub                       system
Breeze GTK theme                               org.gtk.Gtk3theme.Breeze                               6.5.4                            3.22                flathub                       system
KDE Application Platform                       org.kde.Platform                                                                        6.10                flathub                       system

I tried your other suggestions too, unfortunately didn’t work there.

I sincerely apologize for wasting time, it was indeed a permissions problem and I should have checked earlier. I just about enabled everything in flatseal and the flatpaks work flawlessly again. Thank you all for trying.

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