Flatpak apps stopped working today

Hello! I have a few flatpak apps. This morning I fetched the latest system updates (dnf upgrade) and then rebooted, and now my flatpak apps silently fail to open.

I’ve looked in the system journal and also flatpak run -vv but nothing jumps out. The app and system don’t seem to think anything is wrong, but nothing ever appears on the screen.

Here is an example:

✸ flatpak run -vv org.signal.Signal 
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/aron/.local/share/flatpak
F: Opening user flatpak installation at path /home/aron/.local/share/flatpak
F: Opening system flatpak installation at path /var/lib/flatpak
F: Opening user flatpak installation at path /home/aron/.local/share/flatpak
F: Opening system flatpak installation at path /var/lib/flatpak
F: /var/lib/flatpak/runtime/org.freedesktop.Platform/x86_64/23.08/f78b73744458092b80b5084c7fb2880ee9b9bf73fd4e2071105974c96188dff5/files/lib32 does not exist
F: Allocated instance id 3443134932
F: Add defaults in dir /org/signal/Signal/
F: Add locks in dir /org/signal/Signal/
F: Trying to replace with tmpfs: /home/aron/.var/app
F: /home is not a symlink
F: /home/aron is not a symlink
F: /home/aron/.var is not a symlink
F: /home/aron/.var/app is not a symlink
F: Will replace with tmpfs: /home/aron/.var/app
F: Trying to export read/write: /home/aron/.var/app/org.signal.Signal
F: /home is not a symlink
F: /home/aron is not a symlink
F: /home/aron/.var is not a symlink
F: /home/aron/.var/app is not a symlink
F: /home/aron/.var/app/org.signal.Signal is not a symlink
F: Will export read/write: /home/aron/.var/app/org.signal.Signal
F: Trying to replace with tmpfs: /home/aron/.local/share/flatpak
F: /home is not a symlink
F: /home/aron is not a symlink
F: /home/aron/.local is not a symlink
F: /home/aron/.local/share is not a symlink
F: /home/aron/.local/share/flatpak is not a symlink
F: Will replace with tmpfs: /home/aron/.local/share/flatpak
F: Trying to ensure existence of directory: /home/aron
F: /home is not a symlink
F: /home/aron is not a symlink
F: Will ensure existence of directory: /home/aron
F: Converting FlatpakExports to bwrap arguments...
F: "/home/aron" is meant to be a directory
F: Ensuring "/home/aron" is created as a directory
F: "/home/aron/.local/share/flatpak" is meant to be a tmpfs or empty directory
F: Parent of "/home/aron/.local/share/flatpak" is not mapped, creating empty directory
F: "/home/aron/.var/app" is meant to be a tmpfs or empty directory
F: Parent of "/home/aron/.var/app" is not mapped, creating empty directory
F: "/home/aron/.var/app/org.signal.Signal" is meant to be shared (ro or rw) with the container
F: Allowing wayland access
F: Allowing x11 access
F: Allowing pulseaudio access
F: Pulseaudio user configuration file '/home/aron/.config/pulse/client.conf': Error opening file /home/aron/.config/pulse/client.conf: No such file or directory
F: Allowing session-dbus access
F: Allowing system-dbus access

and then it just sits there. But nothing appears on the screen.

I’ve tried other apps (Epiphany and Slack) and they have the same apparent behavior. It’s not clear to me what else I should do for debugging at this point. Does anybody have a suggestion?

Well, rebooting with selinux=0 seems to have worked around the problem.

I don’t know why, though. There wasn’t anything in journalctl -b that suggested an selinux denial was preventing something from working.

I would not turn off SELinux, it’s what keeps you secure. You can disable SELinux transiently by running sudo setenforce 0 and try launching an app and then turn enable SELinux again with sudo setenforce 1 and see if that works around your problem. (getenforce will show you what SELinux status is at the moment). But I wouldn’t boot with SELinux off.

You might not be aware that dnf does not update flatpaks. That is done with the flatpak update command on the cli.

1 Like

Yeah there is very likely a runtime update. flatpak update should help.

I’m aware of dnf versus flatpak. The problem description called out dnf upgrade because that (plus the reboot) is what preceded things breaking.

Also fully up to date with flatpak, but I appreciate the suggestion.

The SELinux workaround was a red herring. It stopped working again after another reboot. Now back with SELinux re-enabled and flatpaks are working again, for the moment.

Not clear yet what’s different between working and not working. There’s no crash or errors reported, so it seems like the “not working” state is actually a “waiting on something” state. I just haven’t figured out what it’s waiting on, nor why it sometimes is able to proceed.

Curious, what kernel are you running? My apps run just fine on 6.6.6-200.fc39.x86_64 and 6.6.6-100.fc38.x86_64, but they hang on 6.6.7-200.fc39.x86_64.

By any chance, do you still have an older kernel installed, and can you try booting into it?

For better or worse, everything seems to be working reliably now. I don’t know why my flatpak-installed applications were hanging rather than starting. It seems clear they were waiting on something, I just don’t know what it was. XWayland? PipeWire via PulseAudio socket?

I’m running 6.6.7-200.fc39.x86_64 now, but was previously running 6.5.6-300.fc39.x86_64. I don’t think my problem was related to kernel version.

I imagine we’re running into the same problem, but I don’t know what to suggest to fix it :slightly_frowning_face:

It happened to me as well several times on Fedora KDE. I thought it is because RPM fusion nvidia drivers are not in sync with flatpak Nvidia drivers.

I’m running Fedora KDE as well, but I don’t have an nVidia GPU.

Currently running an Intel Iris Xe on Framework 12th-gen. SELinux is enabled and enforcing. Also did a reinstall of all packages followed by a full SELinux relabelling of the entire filesystem. Fully uninstalled and reinstalled all flatpaks as well. Nothing interesting shows up in journalctl -f or flatpak run -vv.

It might be statistics at work, but using an older kernel’s been the only thing that’s worked for me. Either that, or I’ve had some bad dice rolls and the Kernel has nothing to do with it at all. A few boots into 6.6.7 have failed, but 6.6.6 seems to work for me. Red herring? Daemons replaced with Demons?