Flatpak apps won't open (hang in background)

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1

Hello community,
I need help to troubleshoot this problem that I’m having for a few months now.
When I try to open any Flatpak application, its startup process hangs and the application is put in the background (seen by Gnome as background app).

The only way for me to get rid of this problem is to:

  1. Click Gnome’s top right menu
  2. Click the (X) to close the background activity. Gnome Shell crashes at this step.
  3. Reboot Fedora
  4. Log back in
$ uname -a
Linux rlussana 6.7.11-200.fc39.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Mar 27 16:50:39 UTC 2024 x86_64 GNU/Linux

Here I try to open Geary with the terminal (-vvv). The command hangs, no crashes:

F: No installations directory in /etc/flatpak/installations.d. Skipping
F: Opening system flatpak installation at path /var/lib/flatpak
F: Opening user flatpak installation at path /home/rlussana/.local/share/flatpak
F: Opening user flatpak installation at path /home/rlussana/.local/share/flatpak
F: Opening system flatpak installation at path /var/lib/flatpak
F: Opening user flatpak installation at path /home/rlussana/.local/share/flatpak
F: Opening system flatpak installation at path /var/lib/flatpak
F: /var/lib/flatpak/runtime/org.fedoraproject.Platform/x86_64/f39/c4c3458676222d94a876eb78ff295a062cb5a00e8e41d465e132e208df68fe1c/files/lib32 does not exist
F: Allocated instance id 1360252587
F: Add values in dir '/org/gnome/Geary/', prefix is '/org/gnome/Geary/'
F: Add defaults in dir /org/gnome/Geary/
F: Add locks in dir /org/gnome/Geary/
F: writing D-Conf values to /home/rlussana/.var/app/org.gnome.Geary/config/glib-2.0/settings/keyfile
F: Allowing dri access
F: Trying to export read/write: /home/rlussana/Downloads
F: /home is not a symlink
F: /home/rlussana is not a symlink
F: /home/rlussana/Downloads is not a symlink
F: Will export read/write: /home/rlussana/Downloads
F: Trying to export read/write: /tmp
F: /tmp is not a symlink
F: Will export read/write: /tmp
F: Trying to export read-only: /home/rlussana/.config/geary
F: Not sharing "/home/rlussana/.config/geary" with sandbox: Unable to open path "/home/rlussana/.config/geary": No such file or directory
F: Trying to export read-only: /home/rlussana/.cache/evolution/addressbook
F: /home is not a symlink
F: /home/rlussana is not a symlink
F: /home/rlussana/.cache is not a symlink
F: /home/rlussana/.cache/evolution is not a symlink
F: /home/rlussana/.cache/evolution/addressbook is not a symlink
F: Will export read-only: /home/rlussana/.cache/evolution/addressbook
F: Trying to replace with tmpfs: /home/rlussana/.var/app
F: /home is not a symlink
F: /home/rlussana is not a symlink
F: /home/rlussana/.var is not a symlink
F: /home/rlussana/.var/app is not a symlink
F: Will replace with tmpfs: /home/rlussana/.var/app
F: Trying to export read/write: /home/rlussana/.var/app/org.gnome.Geary
F: /home is not a symlink
F: /home/rlussana is not a symlink
F: /home/rlussana/.var is not a symlink
F: /home/rlussana/.var/app is not a symlink
F: /home/rlussana/.var/app/org.gnome.Geary is not a symlink
F: Will export read/write: /home/rlussana/.var/app/org.gnome.Geary
F: Trying to replace with tmpfs: /home/rlussana/.local/share/flatpa
kF: /home is not a symlink
F: /home/rlussana is not a symlink
F: /home/rlussana/.local is not a symlink
F: /home/rlussana/.local/share is not a symlink
F: /home/rlussana/.local/share/flatpak is not a symlink
F: Will replace with tmpfs: /home/rlussana/.local/share/flatpak
F: Trying to ensure existence of directory: /home/rlussana
F: /home is not a symlink
F: /home/rlussana is not a symlink
F: Will ensure existence of directory: /home/rlussana
F: Converting FlatpakExports to bwrap arguments...
F: "/home/rlussana" is meant to be a directory
F: Ensuring "/home/rlussana" is created as a directory
F: "/home/rlussana/.cache/evolution/addressbook" is meant to be shared (ro or rw) with the container
F: "/home/rlussana/.local/share/flatpak" is meant to be a tmpfs or empty directory
F: Parent of "/home/rlussana/.local/share/flatpak" is not mapped, creating empty directory
F: "/home/rlussana/.var/app" is meant to be a tmpfs or empty directory
F: Parent of "/home/rlussana/.var/app" is not mapped, creating empty directory
F: "/home/rlussana/.var/app/org.gnome.Geary" is meant to be shared (ro or rw) with the container
F: "/home/rlussana/Downloads" is meant to be shared (ro or rw) with the container
F: "/tmp" is meant to be shared (ro or rw) with the container
F: Allowing wayland access
F: Allowing pulseaudio access
2

Your kernel is not the latest. In the last week fedora has upgraded to the 6.8.4 kernel, so I think a full system upgrade may be suggested which could possibly fix the entire problem.

1 Like
3

I followed your suggestion and it seemed to have fixed the problem for a bit. But now the problem reappeared and it’s still the same as before.

Edit: I’m using Linux 6.8.6-200.fc39.x86_64 #1 SMP PREEMPT_DYNAMIC Sat Apr 13 15:14:23 UTC 2024 x86_64 GNU/Linux

Edit 2: I’ve found a post reporting the same problem as mine on flatpak’s issue page.

Edit 3: When this bug arises Nautilus seems to be very slow to open. I tried looking at Nautilus’ logs by running:

$ G_DEBUG="all" NAUTILUS_DEBUG="All" G_MESSAGES_DEBUG=all nautilus
(org.gnome.Nautilus:17512): GLib-GIO-DEBUG: 13:47:18.263: Using cross-namespace EXTERNAL authentication (this will deadlock if server is GDBus < 2.73.3)
(org.gnome.Nautilus:17512): GLib-GIO-DEBUG: 13:47:18.265: _g_io_module_get_default: Found default implementation gvfs (GDaemonVfs) for ?gio-vfs?

gvfs seems to be slowing Nautilus startup process. Furthermore I can’t open the Trash with Nautilus’ GUI, returns timeout.

Edit 4: I’m suspecting this may be related to having connected an Online Account (Google) that has a Drive folder mounted, maybe this messes with gvfs…

4

I’ll close this since Fedora 40 has been released and seems to have fixed this.

5

I think I have this exact problem. I am on
Fedora Linux 40 (Workstation Edition) x86_64, kernel 6.10.11-200.fc40.x86_64
I didn’t even realize that Nautilus would be slow to open, until I read this thread. Then I tried it, and opening my Documents folder timed out with error. I do not have any online accounts connected, though.

And all Flatpak apps fail to launch for me. No errors, they just hang. For me the problem just started today, with the update to kernel 6.10.11. No issue with 6.10.10.