Zorin 18: Flatpak broken?

General Help
1

I installed the ZorinOS Core update today and now none of my flatpak apps work anymore.
When I start an app, nothing happens. It just hangs until I kill the process.
I tried flatpak repair without success.
Any hints?

2

Whilst I don't think a kernel update, if there was one, would impact severely on Flatpaks, You could test that by booting the previous kernel generic from Grub Menu item "Additional Options for Zorin".
If no difference, just reboot and go back to latest installed kernel.

3

Maybe it helps to run

sudo apt install --reinstall flatpak
4

Thanks, but nothing changed. It also wasn't a kernel update.

5

I also noticed, that conky takes minutes until it appears on the desktop. Conky is not a flatpak package. Other apps behave normal. Strange ...

6

I think we need to find out what was in today's update.
Any Logs? Is there an Update log

7

Good point!

Start-Date: 2026-01-28  06:08:21
Commandline: /usr/bin/unattended-upgrade
Upgrade: libssl-dev:amd64 (3.0.13-0ubuntu3.6, 3.0.13-0ubuntu3.7), libssl3t64:amd64 (3.0.13-0ubuntu3.6, 3.0.13-0ubuntu3.7), openssl:amd64 (3.0.13-0ubuntu3.6, 3.0.13-0ubuntu3.7)
End-Date: 2026-01-28  06:08:23

Start-Date: 2026-01-28  14:27:13
Commandline: aptdaemon role='role-commit-packages' sender=':1.293'
Upgrade: python3-distupgrade:amd64 (1:24.04.27+zorin1, 1:24.04.28+zorin1), libgdm1:amd64 (46.2-1ubuntu1~24.04.5+zorin1, 46.2-1ubuntu1~24.04.6+zorin1), ubuntu-release-upgrader-gtk:amd64 (1:24.04.27+zorin1, 1:24.04.28+zorin1), software-properties-common:amd64 (0.99.49.3+zorin1, 0.99.49.4+zorin1), python3-software-properties:amd64 (0.99.49.3+zorin1, 0.99.49.4+zorin1), gnome-shell:amd64 (46.0-0ubuntu6~24.04.11+zorin1, 46.0-0ubuntu6~24.04.13+zorin1), python-apt-common:amd64 (2.7.7ubuntu5.1+zorin1, 2.7.7ubuntu5.2+zorin1), gdm3:amd64 (46.2-1ubuntu1~24.04.5+zorin1, 46.2-1ubuntu1~24.04.6+zorin1), python3-apt:amd64 (2.7.7ubuntu5.1+zorin1, 2.7.7ubuntu5.2+zorin1), software-properties-gtk:amd64 (0.99.49.3+zorin1, 0.99.49.4+zorin1), gnome-shell-common:amd64 (46.0-0ubuntu6~24.04.11+zorin1, 46.0-0ubuntu6~24.04.13+zorin1), gir1.2-gdm-1.0:amd64 (46.2-1ubuntu1~24.04.5+zorin1, 46.2-1ubuntu1~24.04.6+zorin1), ubuntu-release-upgrader-core:amd64 (1:24.04.27+zorin1, 1:24.04.28+zorin1)
End-Date: 2026-01-28  14:27:18

Start-Date: 2026-01-28  14:27:49
Commandline: aptdaemon role='role-commit-packages' sender=':1.293'
Upgrade: zorin-os-minimal:amd64 (1.7.8, 1.7.9), zorin-os-default-settings:amd64 (18.1.5, 18.1.6), zorin-os-standard:amd64 (1.7.8, 1.7.9), zorin-os-artwork:amd64 (1.7.8, 1.7.9), zorin-os-printer-test-page:amd64 (18.1.5, 18.1.6), zorin-os-desktop:amd64 (1.7.8, 1.7.9), linux-firmware:amd64 (20240318.git3b128b60-0ubuntu2.22, 20240318.git3b128b60-0ubuntu2.23)
End-Date: 2026-01-28  14:27:57

Start-Date: 2026-01-28  14:47:33
Commandline: apt upgrade
Requested-By: hschneider (1000)
Upgrade: libnuma1:amd64 (2.0.18-1build1, 2.0.18-1ubuntu0.24.04.1), numactl:amd64 (2.0.18-1build1, 2.0.18-1ubuntu0.24.04.1)
End-Date: 2026-01-28  14:47:34

Start-Date: 2026-01-28  15:00:41
Commandline: apt install --reinstall flatpak
Requested-By: hschneider (1000)
Reinstall: flatpak:amd64 (1.14.6-1ubuntu0.1)
End-Date: 2026-01-28  15:00:43

Start-Date: 2026-01-28  16:37:25
Commandline: apt install --reinstall flatpak
Requested-By: hschneider (1000)
Reinstall: flatpak:amd64 (1.14.6-1ubuntu0.1)
End-Date: 2026-01-28  16:37:26
8

I did flatpak uninstall --all and re-installed a single app with the same effect. So it's not a dependency issue ...

9

I wonder if this may reveal anything?

journalctl -xe | grep flatpak

You are not running low on disk space by any chance?

I don't use Flatpak or Snap myself, so others may be better source of help.

EDIT: This thread is similar. May be worth a read, but no specific "Solution" was marked. Flatpak just disappeared with all of the installed apps - #8 by Ponce-De-Leon

10

This shows

an 28 16:50:29 nuc15pro flatpak-system-helper[5765]: system: Installed app/io.missioncenter.MissionCenter/x86_64/stable from flathub
Jan 28 16:50:41 nuc15pro systemd[1432]: Started app-flatpak-io.missioncenter.MissionCenter-7562.scope.
Jan 28 16:50:42 nuc15pro flatpak-system-helper[7301]: bwrap: Can't bind mount /oldroot/ on /newroot/: Unable to apply mount flags: remount "/newroot/media/Backup": No such device
Jan 28 16:51:00 nuc15pro systemd[1432]: Started app-flatpak-io.missioncenter.MissionCenter-7609.scope.
Jan 28 17:00:29 nuc15pro systemd[1]: flatpak-system-helper.service: Deactivated successfully.
░░ The unit flatpak-system-helper.service has successfully entered the 'dead' state.
Jan 28 17:00:29 nuc15pro systemd[1]: flatpak-system-helper.service: Consumed 22.965s CPU time.
░░ The unit flatpak-system-helper.service completed and consumed the indicated resources.

Thanks you so much, this nailed it :slight_smile:

My USB backup drive disconnected after reboot, which caused FlatPak to crash for some reason:

.. remount "/newroot/media/Backup": No such device

Reconnected and all apps work again!

3 Likes
11

That was obscure. Glad you are now fixed.

3 Likes
12

ChatGPT explains it like this, which sounds plausible, but still is some kind of obscure :slight_smile: :

That bwrap (Bubblewrap) message usually means:

  • Flatpak tried to expose or remount a directory inside the sandbox
  • That directory points to a mount that no longer exists
  • In your case:
/media/Backup

…which is likely:

  • an external drive
  • a backup disk
  • or a mount that was unplugged or not mounted at the time

Why Flatpak even touches that path

Flatpak automatically:

  • Mirrors parts of your filesystem into the sandbox
  • Tries to preserve mount flags from the host
  • Stumbles if a mount entry exists but the device isn’t present

This is very common on systems with:

  • External drives
  • Old /etc/fstab entries
  • Auto-mounts that aren’t always available

The drive disconnected after the Zorin update reboot. So I supposed the problem there, first.