I have some problems trying to update my flatpaks. I have several applications installed via flatpak (system wide) and from time to time I am updating all of them with the command:

flatpak update -y

This used to work very well, but al of the sudden I get the error:

Flatpak system operation Deploy not allowed for user

Here a complete example:

user:~$ flatpak update -y
Looking for updates… ID Arch Zweig Remote Download 1. [✗] org.kde.WaylandDecoration.QGnomePlatform-decoration x86_64 5.12 flathub 1.0 kB / 56,8 kB 2. [✗] org.kde.WaylandDecoration.QGnomePlatform_decoration.Sources x86_64 5.12 flathub 1.0 kB / 52,6 kB
Warning: Flatpak system operation Deploy not allowed for user
Warning: Flatpak system operation Deploy not allowed for user
Installation complete.

This might be a problem with policykit, the which – as the flatpaks are installed system wide – should have asked me for an administrator password during the update process, but failed to do so.

Can anybody please hint me in the right direction how to solve this problem.

1 Answer

Why not just run flatpak with sudo, as in

sudo flatpak update -y

Another possible workaround is to use setsid:

setsid flatpak update -y

This runs the program in a different session and solved for me a similar problem with the grsync tool.

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