Flatpak app installation or update hangs

Bazzite
1

Hi everyone,

I just installed Bazzite on my desktop (Gigabyte B650 EAGLE AX, AMD Ryzen 7 7800X3D, RTX 5070 Ti), so far so good. However, after some time the system is booted (like an hour) flatpak app installation or update gets stuck at F: Calling system helper: Deploy.

And systemctl status flatpak-system-helper.service

shows

● flatpak-system-helper.service - flatpak system helper
     Loaded: loaded (/usr/lib/systemd/system/flatpak-system-helper.service; static)
    Drop-In: /usr/lib/systemd/system/service.d
             └─10-timeout-abort.conf
     Active: active (running) since Sun 2026-07-19 09:10:53 CEST; 24min ago
 Invocation: a629386a50654d16a5bb5d19eaa5ef57
   Main PID: 46467 (flatpak-system-)
      Tasks: 11 (limit: 37130)
     Memory: 1G (peak: 1.1G)
        CPU: 4.087s
     CGroup: /system.slice/flatpak-system-helper.service
             └─46467 /usr/libexec/flatpak-system-helper

Jul 19 09:15:38 benjazzite flatpak-system-helper[46467]: libostree pull from 'flathub' for runtime/app.polychromatic.controller.Locale/x86_64/stable complete
                                                         security: GPG: commit 
                                                         security: SIGN: disabled 
                                                         non-delta: meta: 1 content: 0
                                                         transfer: secs: 0 size: 592 bytes
Jul 19 09:15:38 benjazzite flatpak-system-helper[46467]: system: Pulled runtime/app.polychromatic.controller.Locale/x86_64/stable from /var/lib/flatpak/repo/tmp/flatpak-cache-TMX9R3/repo-AwHxzo
Jul 19 09:16:07 benjazzite flatpak-system-helper[46467]: libostree pull from 'flathub' for runtime/app.polychromatic.controller.Locale/x86_64/stable complete
                                                         security: GPG: commit 
                                                         security: SIGN: disabled 
                                                         non-delta: meta: 1 content: 0
                                                         transfer: secs: 0 size: 592 bytes
Jul 19 09:16:07 benjazzite flatpak-system-helper[46467]: system: Pulled runtime/app.polychromatic.controller.Locale/x86_64/stable from /var/lib/flatpak/repo/tmp/flatpak-cache-TMFOS3/repo-GrOb0k
Jul 19 09:17:43 benjazzite flatpak-system-helper[46467]: system: Pulled runtime/org.virt_manager.virt_manager.Extension.Qemu/x86_64/stable from /var/lib/flatpak/repo/tmp/flatpak-cache-ADBRS3/repo-NUklbt
Jul 19 09:31:42 benjazzite flatpak-system-helper[46467]: system: Pulled app/io.anytype.anytype/x86_64/stable from /var/lib/flatpak/repo/tmp/flatpak-cache-NI5DS3/repo-UjQPc9
Jul 19 09:34:16 benjazzite flatpak-system-helper[46467]: libostree pull from 'flathub' for app/fm.reaper.Reaper/x86_64/stable complete
                                                         security: GPG: commit 
                                                         security: SIGN: disabled 
                                                         non-delta: meta: 1 content: 0
                                                         transfer: secs: 0 size: 592 bytes
Jul 19 09:34:16 benjazzite flatpak-system-helper[46467]: system: Pulled app/fm.reaper.Reaper/x86_64/stable from /var/lib/flatpak/repo/tmp/flatpak-cache-4N0MS3/repo-O0Ro0F
Jul 19 09:34:22 benjazzite flatpak-system-helper[46467]: libostree pull from 'flathub' for app/fm.reaper.Reaper/x86_64/stable complete
                                                         security: GPG: commit 
                                                         security: SIGN: disabled 
                                                         non-delta: meta: 1 content: 0
                                                         transfer: secs: 0 size: 592 bytes
Jul 19 09:34:23 benjazzite flatpak-system-helper[46467]: system: Pulled app/fm.reaper.Reaper/x86_64/stable from /var/lib/flatpak/repo/tmp/flatpak-cache-VWJAS3/repo-QUTOMq

I tried restarting it but it did not work. I tried flatpak repair but still could not get any flatpak to be installed. Only a reboot fixes the issues for a moment, then it reappears.

Any ideas on what to check/do to to fix this ? Thanks !

2

(post deleted by author)

3

I had similiar problems for the longest time, until I found out that in my case it was the flatpak for smartgit. Maybe this helps: SmartGit Flatpak update hangs in apply_extra / bsdtar for 26_1_038 · Issue #168 · flathub/com.syntevo.SmartGit · GitHub