F43 upgrade breaks Flatpaks

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1

The latest Fedora 43 upgrade broke my Flatpaks. I get this error on flatpak update or any other operation:

Warning: Failed to get revokefs-fuse socket from system-helper: Could not activate remote peer 'org.freedesktop.Flatpak.SystemHelper': startup job failed
Error: Could not activate remote peer 'org.freedesktop.Flatpak.SystemHelper': startup job failed

Anyone got any ideas on how to fix this?

3

Another user had a similar issue, which got fixed by running sudo flatpak update (though sudo is not needed for updating flatpaks).

So this seems to be a reproducible issue now.

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4

I had timeout errors this morning when updating flatpaks from Flathub. Just tried it again and now it works. No idea if this is related to the OP’s issue.

5

I’ve had the same issue when running flatpak update today. It also gave an SELinux alert at the same time:

SELinux is preventing (waydroid) from execute access on the file /usr/libexec/flatpak-system-helper.

Running sudo flatpak update worked with no errors.

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6

Okay, sudo flatpak update works as expected. Bunch of remote fetch errors without sudo, so maybe SELinux is to blame. Well, temporary fix achieved: prepend sudo.

8

Quoting https://docs.flathub.org/docs/for-users/user-vs-system-install

Flatpak applications can be installed either per-user or system-wide. The difference is that per-user installations are only available to the user that installed them, while system-wide installations are available to all users on the system. System-wide installations can be updated by any user with administrator privileges. The choice between per-user and system-wide installations depends on the use case.

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9

Have you done
sudo flatpak repair

And then see if it works normally?

10

Having the same issue on one of my fedora machines. tried the following to no avail:

  • flatpak remote-add --if-not-exists --user flathub https://dl.flathub.org/repo/flathub.flatpakrepo
  • flatpak repair
  • sudo flatpak repair
  • sudo dnf reinstall flatpak
  • sudo restorecon -vR /
  • sudo fixfiles -B onboot

Nothing changed, so far updating flatpaks without sudo fails consistently, which unfortunately breaks many maintenance scripts.

11

System-wide installations can be updated by any user with administrator privileges.

Yes, but it doesn’t normally require sudo to do so. You just need to be in an appropriate group (probably ‘wheel’), then you can run flatpak update to update system-wide installations.

So if the update only works with sudo, then something unexpected is going on.

12

I’ve tried Flatpak repair but that didn’t help.

Then I switched SELinux to permissive mode rebooted and now flatpak runs as normal. After switching it back on to enforcing I still can’t replicate the issue. So that seems to have fixed it, somehow?

13

I haven’t tried this in F43. Previously, running flatpak update on system-wide installations resulted in multiple password prompts – one for each component being updated.

14

Interesting, works fine for me on F42! (and also did on F41).

15

I did not observe this on earlier versions either.

16

did you set the permissive mode temporarily using setenforce or did you edit /etc/selinux/config?

17

I did sudoedit /etc/selinux/config, changed SELINUX= , then rebooted.
So admittedly it could have been something else like the flatpak repair which solved it, if that just needed a reboot to take effect.

18

Just tried removing a flatpak with Origin=fedora and Installation=system in Fedora 43 without sudo. I did not get any password prompt.

19

I have another machine still on F42 which always asks for authentication on every package if flatpak is not run with sudo. Although my user there is a wheel user. I haven’t looked into it before since it’s not really been much of an issue, that machine updates fine when done automatically and I leave it at that.

==== AUTHENTICATING FOR org.freedesktop.Flatpak.modify-repo ====
Authentication is required to modify a system repository
Authenticating as: Username (username)
Password:

This laptop hasn’t prompted for a password before, at least since updating to F43 and I don’t remember it occurring on F42 either. Weird.

20

I’ve never had an auth prompt for flatpak. I run it as my login user (non-elevated, but member of wheel group). I’ve also tried everything except mentioned by @alghostzx except sudo fixfiles -B onboot.

I just tried the suggestion from @j-strawberry to switch SELinux modes. After sudo setenforce 0 (and no reboot), flatpak update runs as expected from unprivileged user. I’ll set SELinux policy to permissive, should keep flatpaks working on user account on each boot.

Edit: sudo setenforce 1 doesn’t reproduce the error, just as @j-strawberry mentioned. So solution was sudo setenforce 0, and then optionally sudo setenforce 1. Setting SELinux to enforce yields errors on uninstalls which aren’t present in permissive mode. Will update with behavior on next boot.

21

Can confirm that doing sudo setenforce 0;flatpak update;sudo setenforce 1 does indeed make Flatpak updates work, confirming that the problem, somehow, lies in the SELinux policy. I know NOTHING of SELinux, so I can’t troubleshoot beyond this.

I’ve also never had an auth prompt for Flatpak, and I don’t know why other users are trying to hijack this topic with this unrelated issue to the matter at hand.