Discover randomly lists lots of Flatpak packages as ready to update, yet fails to update them, then they disappear. Why? How?

Errata

I’d file it at Log in to KDE Bugtracking System, but I don’t really understand whether it’s a bug because I don’t understand why it’s happening.

Environment

kinfo
Operating System: Fedora Linux 40
KDE Plasma Version: 6.1.4
KDE Frameworks Version: 6.5.0
Qt Version: 6.7.2
Kernel Version: 6.10.10-200.fc40.x86_64 (64-bit)
Graphics Platform: Wayland
Processors: 12 × AMD Ryzen 5 7600X 6-Core Processor
Memory: 30.5 GiB of RAM
Graphics Processor: AMD Radeon RX 5700
Manufacturer: ASRock
Product Name: X670E Taichi
dnf info plasma-discover
PS /home/RokeJulianLockhart> dnf info plasma-discover
Last metadata expiration check: 0:54:30 ago on Wed 18 Sep 2024 22:40:35 BST.
Installed Packages
Name         : plasma-discover
Version      : 6.1.4
Release      : 1.fc40
Architecture : x86_64
Size         : 1.7 M
Source       : plasma-discover-6.1.4-1.fc40.src.rpm
Repository   : @System
From repo    : updates
URL          : https://invent.kde.org/plasma/discover
flatpak list
PS /home/RokeJulianLockhart> flatpak list
Name                                              Application ID                                      Version                              Branch                  Origin                     Installation
Bitwarden                                         com.bitwarden.desktop                               2024.8.2                             stable                  flathub                    system
Gittyup                                           com.github.Murmele.Gittyup                          v1.4.0                               stable                  gittyup-origin             user
Eyedropper                                        com.github.finefindus.eyedropper                    2.0.1                                stable                  flathub                    system
Czkawka                                           com.github.qarmin.czkawka                           6.1.0                                stable                  flathub                    system
Proton VPN                                        com.protonvpn.www                                   4.4.4                                stable                  flathub                    system
Goldwarden                                        com.quexten.Goldwarden                              v0.3.3                               stable                  flathub                    system
Spotify                                           com.spotify.Client                                  1.2.42.290.g242057a2                 stable                  flathub                    system
Stremio Service                                   com.stremio.Service                                 0.1.13                               stable                  flathub                    system
Stremio                                           com.stremio.Stremio                                 4.4.168                              stable                  flathub                    system
Valve Corporation                                 com.valvesoftware.Steam                             1.0.0.79                             stable                  flathub                    system
Vesktop                                           dev.vencord.Vesktop                                 1.5.3                                stable                  flathub                    system
AdwSteamGtk                                       io.github.Foldex.AdwSteamGtk                        0.6.11                               stable                  flathub                    system
AppImage Pool                                     io.github.prateekmedia.appimagepool                 5.1.0                                stable                  flathub                    system
Gear Lever                                        it.mijorus.gearlever                                2.0.7                                stable                  flathub                    system
Freedesktop Platform                              org.freedesktop.Platform                            freedesktop-sdk-22.08.26             22.08                   flathub                    system
Freedesktop Platform                              org.freedesktop.Platform                                                                 23.08                   flathub                    system
i386                                              org.freedesktop.Platform.Compat.i386                                                     23.08                   flathub                    system
Mesa                                              org.freedesktop.Platform.GL.default                 24.0.9                               22.08                   flathub                    system
Mesa (Extra)                                      org.freedesktop.Platform.GL.default                 24.0.9                               22.08-extra             flathub                    system
Mesa                                              org.freedesktop.Platform.GL.default                 24.2.1                               23.08                   flathub                    system
Mesa (Extra)                                      org.freedesktop.Platform.GL.default                 24.2.1                               23.08-extra             flathub                    system
Mesa                                              org.freedesktop.Platform.GL.default                 24.2.2                               24.08                   flathub                    system
Mesa (Extra)                                      org.freedesktop.Platform.GL.default                 24.2.2                               24.08extra              flathub                    system
Mesa                                              org.freedesktop.Platform.GL32.default               24.2.1                               23.08                   flathub                    system
Mesa (Extra)                                      org.freedesktop.Platform.GL32.default               24.2.1                               23.08-extra             flathub                    system
openh264                                          org.freedesktop.Platform.openh264                   2.1.0                                2.2.0                   flathub                    system
openh264                                          org.freedesktop.Platform.openh264                   2.4.1                                2.4.1                   flathub                    system
Freedesktop SDK                                   org.freedesktop.Sdk                                                                      23.08                   flathub                    system
OpenJDK 17 SDK Extension                          org.freedesktop.Sdk.Extension.openjdk17                                                  23.08                   flathub                    system
GNOME Application Platform version 45             org.gnome.Platform                                                                       45                      flathub                    system
GNOME Application Platform version 46             org.gnome.Platform                                                                       46                      flathub                    system
GNOME Application Platform version 47             org.gnome.Platform                                                                       47                      flathub                    system
Godot Engine (C#/.NET)                            org.godotengine.GodotSharp                          4.3                                  stable                  flathub                    system
Breeze GTK theme                                  org.gtk.Gtk3theme.Breeze                            6.1.5                                3.22                    flathub                    system
KDE Application Platform                          org.kde.Platform                                                                         5.15-23.08              flathub                    system
KDE Application Platform                          org.kde.Platform                                                                         6.7                     flathub                    system
KDE Software Development Kit                      org.kde.Sdk                                                                              6.7                     flathub                    system
Prism Launcher                                    org.prismlauncher.PrismLauncher                     8.4                                  stable                  flathub                    system

I can’t answer this - I think if I used Fedora I’d run updates with sudo dnf update instead…

You could also try installing topgrade (I currently have topgrade 15.0.0-2) which is a very nice and fairly cross-platform tool to catch all kinds of updates.

Also, to check flatpaks on their own, you can just use

 flatpak update -y && flatpak remove --unused -y 

Overall, (on Arch) we don’t use discover - it works best with the Debian base - so I’d suggest you go with dnf for your updates.

1 Like

I want to say I saw something similar happen on my Fedora KDE system, and all I needed to do was run a flatpak update from a terminal.

IIRC (but that’s a big if!) the issue was that an installed Flatpak had a version update which added a new dependency, and I suspect PackageKit wasn’t able to handle that, since the new dependency needed user approval in order to be installed but that question couldn’t be interactively presented.

tl;dr check flatpak update and see if it asks to install a new Flatpak package?

2 Likes

Sounds right - don’t trust Discover on Fedora.

Unfortunately, @ben2talk and @johnandmegh, I’ve tried flatpak update, and there weren’t any listed updates, which was perplexing. I’ve also tried remove --unused, which solely tried to remove Breeze-Dark due to it being EOL, but the theme had dependencies that prevented it:

flatpak update -y
Looking for updates…

Nothing to do.
flatpak remove --unused -y
These runtimes in installation 'system' are pinned and won't be removed; see flatpak-pin(1):
  runtime/org.kde.Sdk.Debug/x86_64/6.7
  runtime/org.kde.Sdk/x86_64/6.7
Nothing unused to uninstall

Because it uses the PackageKit abstraction, rather than a direct integration with dnf?

1 Like

I’m not pessimistic about Discover on Fedora overall - I normally use it for updates, unless there’s a kernel or Nvidia driver update on my Nvidia systems (since AFAIK the reboot-update-reboot “offline” mechanism doesn’t allow enough time for the kernel modules to finish building), and I haven’t had any major issues.

Back to your specific situation - if flatpak update is telling you there are no updates, and Discover is telling you there are, then that must mean that PackageKit is “stuck” somehow thinking that it doesn’t need to go back out to the core tools (dnf and flatpak) to get fresh info, when it really does. Try pkcon refresh force and see if that helps?

1 Like

Basically, I use Manjaro and I’m not quite so sure about Fedora… for me it’s pamac which will update system/AUR/Flatpaks.

1 Like

@johnandmegh, I’ll mark that as the solution because that’s the sole conclusion I come to either, and the issue doesn’t reproduce consistently enough for me to test your proposed solution.

Irrespective, should it reproduce, I’ll report whether it works:

Ah - yeah, I don’t know that I’d generalize from Manjaro to…pretty much any other distribution, in terms of how updates are best handled :slight_smile:

Outside of the Fedora akmods Nvidia case, AFAIK Discover works well (or, to the point of this thread, as well as PackageKit can support) for updates in most distributions that are set up for PackageKit-handled updates, like Debian, Ubuntu, Fedora, etc.

Where it will fall down is largely where the distribution / repository / package manager setup is such that specific commands must be issued, and specific interactive steps must be taken, in order to update successfully. Prominent examples in that case would be openSUSE Tumbleweed (zypper dup is the only approved way to update system software) and Arch.

@johnandmegh, it doesn’t work, unfortunately:


Interestingly, I’ve ascertained that when Discover does this, it also doesn’t appear to acknowledge any updates from dnf, even if a multitude are available:

PS /home/RokeJulianLockhart> sudo dnf upgrade
Last metadata expiration check: 1:48:31 ago on Sat 21 Sep 2024 23:06:50 BST.
Dependencies resolved.

 Problem 1: package qt5-qtwebengine-freeworld-5.15.17-1.fc40.x86_64 from @System requires qt5-qtbase(x86-64) = 5.15.14, but none of the providers can be installed
  - cannot install both qt5-qtbase-5.15.15-1.fc40.x86_64 from updates and qt5-qtbase-5.15.14-6.fc40.x86_64 from @System
  - cannot install the best update candidate for package qt5-qtwebengine-freeworld-5.15.17-1.fc40.x86_64
  - cannot install the best update candidate for package qt5-qtbase-5.15.14-6.fc40.x86_64
 Problem 2: problem with installed package qt5-qtwebengine-freeworld-5.15.17-1.fc40.x86_64
  - package qt5-qtwebengine-freeworld-5.15.17-1.fc40.x86_64 from @System requires qt5-qtbase(x86-64) = 5.15.14, but none of the providers can be installed
  - package qt5-qtwebengine-freeworld-5.15.17-1.fc40.x86_64 from rpmfusion-free-updates requires qt5-qtbase(x86-64) = 5.15.14, but none of the providers can be installed
  - cannot install both qt5-qtbase-5.15.15-1.fc40.x86_64 from updates and qt5-qtbase-5.15.14-6.fc40.x86_64 from @System
  - package kddockwidgets-1.7.0-13.fc40.x86_64 from updates requires qt5-qtbase(x86-64) = 5.15.15, but none of the providers can be installed
  - cannot install the best update candidate for package kddockwidgets-1.7.0-11.fc40.x86_64
===============================================================================================================================================================================================================================================================================
 Package                                                                     Architecture                               Version                                               Repository                                                                                  Size
===============================================================================================================================================================================================================================================================================
Installing:
 kernel                                                                      x86_64                                     6.10.11-200.fc40                                      updates-testing                                                                            177 k
 kernel-core                                                                 x86_64                                     6.10.11-200.fc40                                      updates-testing                                                                             17 M
 kernel-modules                                                              x86_64                                     6.10.11-200.fc40                                      updates-testing                                                                             63 M
 kernel-modules-core                                                         x86_64                                     6.10.11-200.fc40                                      updates-testing                                                                             38 M
 kernel-modules-extra                                                        x86_64                                     6.10.11-200.fc40                                      updates-testing                                                                            2.9 M
Upgrading:
 ImageMagick                                                                 x86_64                                     1:7.1.1.38-1.fc40                                     updates-testing                                                                             73 k
 ImageMagick-c++                                                             x86_64                                     1:7.1.1.38-1.fc40                                     updates-testing                                                                            176 k
 ImageMagick-libs                                                            x86_64                                     1:7.1.1.38-1.fc40                                     updates-testing                                                                            2.6 M
 LibRaw                                                                      x86_64                                     0.21.3-1.fc40                                         updates-testing                                                                            411 k
 coolercontrol                                                               x86_64                                     1.4.1-1.fc40                                          copr:copr.fedorainfracloud.org:codifryed:CoolerControl                                     4.4 M
 coolercontrol-liqctld                                                       x86_64                                     1.4.1-1.fc40                                          copr:copr.fedorainfracloud.org:codifryed:CoolerControl                                      74 k
 coolercontrold                                                              x86_64                                     1.4.1-1.fc40                                          copr:copr.fedorainfracloud.org:codifryed:CoolerControl                                     6.0 M
 firefox                                                                     x86_64                                     130.0.1-1.fc40                                        updates                                                                                     71 M
 firefox-langpacks                                                           x86_64                                     130.0.1-1.fc40                                        updates                                                                                     47 M
 gstreamer1                                                                  i686                                       1.24.8-1.fc40                                         updates-testing                                                                            1.7 M
 gstreamer1                                                                  x86_64                                     1.24.8-1.fc40                                         updates-testing                                                                            1.6 M
 gstreamer1-plugin-libav                                                     x86_64                                     1.24.8-1.fc40                                         updates-testing                                                                            206 k
 gstreamer1-plugin-openh264                                                  x86_64                                     1.24.8-1.fc40                                         updates-testing                                                                             37 k
 gstreamer1-plugins-bad-free                                                 x86_64                                     1.24.8-1.fc40                                         updates-testing                                                                            2.8 M
 gstreamer1-plugins-bad-free-libs                                            x86_64                                     1.24.8-1.fc40                                         updates-testing                                                                            927 k
 gstreamer1-plugins-base                                                     x86_64                                     1.24.8-1.fc40                                         updates-testing                                                                            2.2 M
 gstreamer1-plugins-good                                                     x86_64                                     1.24.8-1.fc40                                         updates-testing                                                                            2.4 M
 gstreamer1-plugins-good-gtk                                                 x86_64                                     1.24.8-1.fc40                                         updates-testing                                                                             33 k
 gstreamer1-plugins-good-qt                                                  x86_64                                     1.24.8-1.fc40                                         updates-testing                                                                             71 k
 gstreamer1-plugins-good-qt6                                                 x86_64                                     1.24.8-1.fc40                                         updates-testing                                                                             81 k
 gstreamer1-plugins-ugly-free                                                x86_64                                     1.24.8-1.fc40                                         updates-testing                                                                            247 k
 m17n-db                                                                     noarch                                     1.8.8-1.fc40                                          updates-testing                                                                            818 k
 ostree                                                                      x86_64                                     2024.8-1.fc40                                         updates-testing                                                                            278 k
 ostree-libs                                                                 x86_64                                     2024.8-1.fc40                                         updates-testing                                                                            464 k
 perf                                                                        x86_64                                     6.10.11-200.fc40                                      updates-testing                                                                            2.4 M
 pipewire                                                                    i686                                       1.0.8-1.fc40                                          updates                                                                                    122 k
 pipewire                                                                    x86_64                                     1.0.8-1.fc40                                          updates                                                                                    122 k
 pipewire-alsa                                                               i686                                       1.0.8-1.fc40                                          updates                                                                                     58 k
 pipewire-alsa                                                               x86_64                                     1.0.8-1.fc40                                          updates                                                                                     56 k
 pipewire-gstreamer                                                          x86_64                                     1.0.8-1.fc40                                          updates                                                                                     64 k
 pipewire-jack-audio-connection-kit                                          x86_64                                     1.0.8-1.fc40                                          updates                                                                                     15 k
 pipewire-jack-audio-connection-kit-libs                                     x86_64                                     1.0.8-1.fc40                                          updates                                                                                    134 k
 pipewire-libs                                                               i686                                       1.0.8-1.fc40                                          updates                                                                                    1.9 M
 pipewire-libs                                                               x86_64                                     1.0.8-1.fc40                                          updates                                                                                    1.8 M
 pipewire-pulseaudio                                                         x86_64                                     1.0.8-1.fc40                                          updates                                                                                    197 k
 pipewire-utils                                                              x86_64                                     1.0.8-1.fc40                                          updates                                                                                    335 k
 unicode-ucd                                                                 noarch                                     16.0.0-1.fc40                                         updates-testing                                                                            6.2 M
Removing:
 kernel                                                                      x86_64                                     6.10.8-200.fc40                                       @updates-testing                                                                             0  
 kernel-core                                                                 x86_64                                     6.10.8-200.fc40                                       @updates-testing                                                                            69 M
 kernel-modules                                                              x86_64                                     6.10.8-200.fc40                                       @updates-testing                                                                            62 M
 kernel-modules-core                                                         x86_64                                     6.10.8-200.fc40                                       @updates-testing                                                                            36 M
 kernel-modules-extra                                                        x86_64                                     6.10.8-200.fc40                                       @updates-testing                                                                           2.7 M
Skipping packages with conflicts:
(add '--best --allowerasing' to command line to force their upgrade):
 qt5-qtbase                                                                  x86_64                                     5.15.15-1.fc40                                        updates                                                                                    3.6 M
Skipping packages with broken dependencies:
 kddockwidgets                                                               x86_64                                     1.7.0-13.fc40                                         updates                                                                                    398 k

Transaction Summary
===============================================================================================================================================================================================================================================================================
Install   5 Packages
Upgrade  37 Packages
Remove    5 Packages
Skip      2 Packages

Total download size: 281 M
Is this ok [y/N]:
1 Like

Hmm, then maybe the ultimate test - if you try sudo pkcon update at that point to try performing the update with PackageKit directly… does PackageKit tell you there are available updates?

If it does, and offers to / successfully completes them, then it’s probably a Discover bug - if PackageKit is also out of sync with dnf there, then it’s probably a PackageKit bug?

1 Like
  1. PS /home/RokeJulianLockhart> sudo pkcon update
    [sudo] password for RokeJulianLockhart: 
    Getting updates                         [=========================]         
    Finished                                [=========================]         
    No packages require updating to newer versions.
    

@johnandmegh, I shan’t be surprised if it’s a bug with either, but I find that most of Discover’s bugs are due to hideous PackageKit behaviour. Unfortunately, the logs aren’t revealing in this case:

org.kde.plasma.libdiscover.backend.flatpak: Failed to install FlatpakResource::NotAFile runtime/org.gtk.Gtk3theme.Breeze-Dark/x86_64/3.22 : "org.gtk.Gtk3theme.Breeze-Dark/x86_64/3.22 not installed"

I’ll try reporting it to KDE first, and they’ll probably triage it as upstream. Thanks for the assistance.


https://wim.nl.tab.digital/apps/tasks/#/collections/all/tasks/D2F7E4AC-9012-4812-A16E-3BBB3C01C3DD.ics