Automatic flatpak update systemd service fails

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1

It works fine when I start the service manually.

flatpak-update.sh

#!/usr/bin/env bash

notify-send --app-name="Flatpak Automatic Update" \
    --icon="system-software-update" --hint="string:desktop-entry:discover" \
    "Updating applications..."

(flatpak update --assumeyes --noninteractive && \
    notify-send --app-name="Flatpak Automatic Update" \
        --icon="system-software-update" \
        --hint="string:desktop-entry:discover" \
        "Application updates have been successfully installed") || \
    notify-send --app-name="Flatpak Automatic Update" \
        --icon="system-software-update" \
        --hint="string:desktop-entry:discover" \
        "Failed to update applications"

cat update-system-flatpaks.service

[Unit]
Description=Update system Flatpaks
After=graphical-session.target network-online.target
Wants=network-online.target

[Service]
Type=oneshot
ExecStart=%h/.local/bin/flatpak-updates.sh

[Install]
WantedBy=default.target

cat update-system-flatpaks.timer

[Unit]
Description=Update system Flatpaks every Saturday after login

[Timer]
OnCalendar=Sat 10:00
Persistent=true

[Install]
WantedBy=timers.target

systemctl --user status update-system-flatpaks

○ update-system-flatpaks.service - Update system Flatpaks
     Loaded: loaded (/home/rob/.config/systemd/user/update-system-flatpaks.service; disabled; preset: disabled)
    Drop-In: /usr/lib/systemd/user/service.d
             └─10-timeout-abort.conf
     Active: inactive (dead) since Sat 2025-05-17 10:14:21 CEST; 6h ago
 Invocation: 67e540a8e18a4b3c83aee6708aeb8da6
TriggeredBy: ● update-system-flatpaks.timer
    Process: 177183 ExecStart=/home/rob/.local/bin/flatpak-updates.sh (code=exited, status=0/SUCCESS)
   Main PID: 177183 (code=exited, status=0/SUCCESS)
   Mem peak: 6.7M
        CPU: 116ms

May 17 10:14:20 hp-laptop systemd[1517]: Starting update-system-flatpaks.service - Update system Flatpaks...
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.kde.Platform/x86_64/6.9 is already installed: No such ref 'runtime/org.kde.Platform/x86_64/6.9' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.kde.Platform/x86_64/6.8 is already installed: No such ref 'runtime/org.kde.Platform/x86_64/6.8' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.kde.Platform.Locale/x86_64/6.9 is already installed: No such ref 'runtime/org.kde.Platform.Locale/x86_64/6.9' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.kde.Platform.Locale/x86_64/6.8 is already installed: No such ref 'runtime/org.kde.Platform.Locale/x86_64/6.8' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.kde.KStyle.Adwaita/x86_64/6.8 is already installed: No such ref 'runtime/org.kde.KStyle.Adwaita/x86_64/6.8' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.gtk.Gtk3theme.Breeze/x86_64/3.22 is already installed: No such ref 'runtime/org.gtk.Gtk3theme.Breeze/x86_64/3.22' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.gnome.Platform/x86_64/48 is already installed: No such ref 'runtime/org.gnome.Platform/x86_64/48' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.gnome.Platform.Locale/x86_64/48 is already installed: No such ref 'runtime/org.gnome.Platform.Locale/x86_64/48' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.freedesktop.Platform/x86_64/24.08 is already installed: No such ref 'runtime/org.freedesktop.Platform/x86_64/24.08' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.freedesktop.Platform.openh264/x86_64/2.5.1 is already installed: No such ref 'runtime/org.freedesktop.Platform.openh264/x86_64/2.5.1' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.freedesktop.Platform.VAAPI.Intel/x86_64/24.08 is already installed: No such ref 'runtime/org.freedesktop.Platform.VAAPI.Intel/x86_64/24.08' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.freedesktop.Platform.Locale/x86_64/24.08 is already installed: No such ref 'runtime/org.freedesktop.Platform.Locale/x86_64/24.08' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.freedesktop.Platform.GL.default/x86_64/24.08extra is already installed: No such ref 'runtime/org.freedesktop.Platform.GL.default/x86_64/24.08extra' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/org.freedesktop.Platform.GL.default/x86_64/24.08 is already installed: No such ref 'runtime/org.freedesktop.Platform.GL.default/x86_64/24.08' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/net.ankiweb.Anki.Locale/x86_64/stable is already installed: No such ref 'runtime/net.ankiweb.Anki.Locale/x86_64/stable' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/com.chatterino.chatterino.Locale/x86_64/stable is already installed: No such ref 'runtime/com.chatterino.chatterino.Locale/x86_64/stable' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since runtime/com.bitwarden.desktop.Locale/x86_64/stable is already installed: No such ref 'runtime/com.bitwarden.desktop.Locale/x86_64/stable' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since app/org.nicotine_plus.Nicotine/x86_64/stable is already installed: No such ref 'app/org.nicotine_plus.Nicotine/x86_64/stable' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since app/net.ankiweb.Anki/x86_64/stable is already installed: No such ref 'app/net.ankiweb.Anki/x86_64/stable' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since app/com.chatterino.chatterino/x86_64/stable is already installed: No such ref 'app/com.chatterino.chatterino/x86_64/stable' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since app/com.brave.Browser/x86_64/stable is already installed: No such ref 'app/com.brave.Browser/x86_64/stable' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: F: Warning: Treating remote fetch error as non-fatal since app/com.bitwarden.desktop/x86_64/stable is already installed: No such ref 'app/com.bitwarden.desktop/x86_64/stable' in remote flathub
May 17 10:14:21 hp-laptop flatpak-updates.sh[177241]: Nothing to do.
May 17 10:14:21 hp-laptop systemd[1517]: Finished update-system-flatpaks.service - Update system Flatpaks.
3

Could the problem be that network-online.target isn’t available to user units, so the service starts before it has a working network connection?

For example as in this Podman issue and this systemd enhancement request.

4

Changed the service to check for internet in the shell script (not sure if there is a better way of doing this)

rob@hp-laptop:~/.config/systemd/user$ cat update-flatpaks.service
[Unit]
Description=Update Flatpaks retry hourly on fail
Requires=graphical-session.target
After=graphical-session.target

[Service]
Type=oneshot
ExecStart=%h/.local/libexec/update-flatpaks.sh
Restart=on-failure
RestartSec=3600
rob@hp-laptop:~/.config/systemd/user$ cat update-flatpaks.timer
[Unit]
Description=Update system Flatpaks every Saturday at 10:00 after login

[Timer]
OnCalendar=Sat 10:00
Persistent=true

[Install]
WantedBy=timers.target

rob@hp-laptop:~/.config/systemd/user$ cat ~/.local/libexec/update-flatpaks.sh
#!/usr/bin/env bash

if [ "$(nmcli networking connectivity)" != "full" ] ; then
    exit 1
fi

notify-send --app-name="Flatpak Automatic Update" \
    --icon="system-software-update" --hint="string:desktop-entry:discover" \
    "Updating applications..."

(flatpak update --assumeyes --noninteractive && \
    notify-send --app-name="Flatpak Automatic Update" \
        --icon="system-software-update" \
        --hint="string:desktop-entry:discover" \
        "Application updates have been successfully installed") || \
    notify-send --app-name="Flatpak Automatic Update" \
        --icon="system-software-update" \
        --hint="string:desktop-entry:discover" \
        "Failed to update applications"
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