Fedora consistently fails with all updates (2/14/25)

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1

Rebooting every 5 minutes

Journal

Feb 14 14:15:34 mini-pc PackageKit[2449]: resolve transaction /96791_ddcedbde from uid 1000 finished with success after 23ms
Feb 14 14:15:34 mini-pc PackageKit[2449]: resolve transaction /96792_abddedbb from uid 1000 finished with success after 16ms
Feb 14 14:15:34 mini-pc systemd[1]: Starting flatpak-system-helper.service - flatpak system helper...
Feb 14 14:15:34 mini-pc systemd[1]: Started flatpak-system-helper.service - flatpak system helper.
Feb 14 14:15:34 mini-pc audit[1]: SERVICE_START pid=1 uid=0 auid=4294967295 ses=4294967295 subj=system_u:system_r:init_t:s0 msg='unit=flatpak-system-helper comm="systemd" exe="/usr/lib/systemd/s>
Feb 14 14:15:35 mini-pc PackageKit[2449]: get-updates transaction /96793_ccaccebd from uid 1000 finished with success after 1414ms
Feb 14 14:15:35 mini-pc PackageKit[2449]: resolve transaction /96794_cdaaaebe from uid 1000 finished with success after 53ms
Feb 14 14:15:36 mini-pc PackageKit[2449]: search-file transaction /96795_dadbebcb from uid 1000 finished with success after 353ms
Feb 14 14:15:36 mini-pc PackageKit[2449]: search-file transaction /96796_dddcbded from uid 1000 finished with success after 23ms
Feb 14 14:15:36 mini-pc PackageKit[2449]: search-file transaction /96797_bbbeceac from uid 1000 finished with success after 21ms
Feb 14 14:15:36 mini-pc PackageKit[2449]: get-updates transaction /96798_dabcebee from uid 1000 finished with success after 199ms

Feb 14 14:15:37 mini-pc appimagelauncherd[1939]: Directories to watch disappeared, unintegrating AppImages formerly found in there
Feb 14 14:15:37 mini-pc PackageKit[2449]: get-updates transaction /96799_dcdbeabb from uid 1000 finished with success after 218ms
Feb 14 14:15:38 mini-pc PackageKit[2449]: get-updates transaction /96800_adbcbcbb from uid 1000 finished with success after 191ms
Feb 14 14:15:38 mini-pc systemd[1]: Stopping user@42.service - User Manager for UID 42...
Feb 14 14:15:38 mini-pc systemd[1856]: Activating special unit exit.target...
Feb 14 14:15:38 mini-pc systemd[1856]: Stopped target default.target - Main User Target.
Feb 14 14:15:38 mini-pc systemd[1856]: Stopping pipewire-pulse.service - PipeWire PulseAudio...
Feb 14 14:15:38 mini-pc systemd[1856]: Stopped pipewire-pulse.service - PipeWire PulseAudio.
Feb 14 14:15:38 mini-pc systemd[1856]: Stopping wireplumber.service - Multimedia Service Session Manager...
Feb 14 14:15:38 mini-pc wireplumber[2714]: wireplumber: stopped by signal: Terminated
Feb 14 14:15:38 mini-pc wireplumber[2714]: wireplumber: disconnected from pipewire
Feb 14 14:15:38 mini-pc systemd[1856]: Stopped wireplumber.service - Multimedia Service Session>
Feb 14 14:15:38 mini-pc systemd[1856]: Stopping pipewire.service - PipeWire Multimedia Service.>
Feb 14 14:15:38 mini-pc systemd[1856]: Stopped pipewire.service - PipeWire Multimedia Service.
Feb 14 14:15:38 mini-pc systemd[1856]: Stopped target basic.target - Basic System.
Feb 14 14:15:38 mini-pc systemd[1856]: Stopped target paths.target - Paths.
Feb 14 14:15:38 mini-pc systemd[1856]: Stopped target sockets.target - Sockets.Feb 14 14:15:38 mini-pc systemd[1856]: Stopped target timers.target - Timers.
Feb 14 14:15:38 mini-pc systemd[1856]: Stopped systemd-tmpfiles-clean.timer - Daily Cleanup of >
Feb 14 14:15:38 mini-pc systemd[1856]: Closed pipewire-pulse.socket - PipeWire PulseAudio.
Feb 14 14:15:38 mini-pc systemd[1856]: Closed pipewire.socket - PipeWire Multimedia System Sock>
Feb 14 14:15:38 mini-pc systemd[1856]: Closed snapd.session-agent.socket - REST API socket for >
Feb 14 14:15:38 mini-pc dbus-broker[1988]: Dispatched 283 messages @ 4(±22)μs / message.
Feb 14 14:15:38 mini-pc systemd[1856]: Stopping dbus-broker.service - D-Bus User Message Bus...
Feb 14 14:15:38 mini-pc systemd[1856]: Stopped systemd-tmpfiles-setup.service - Create User Fil>
Feb 14 14:15:38 mini-pc systemd[1856]: Stopped dbus-broker.service - D-Bus User Message Bus.
Feb 14 14:15:38 mini-pc systemd[1856]: Removed slice session.slice - User Core Session Slice.
Feb 14 14:15:38 mini-pc systemd[1856]: Closed dbus.socket - D-Bus User Message Bus Socket.
Feb 14 14:15:38 mini-pc systemd[1856]: Removed slice app.slice - User Application Slice.
Feb 14 14:15:38 mini-pc systemd[1856]: Reached target shutdown.target - Shutdown.
Feb 14 14:15:38 mini-pc systemd[1856]: Finished systemd-exit.service - Exit the Session.
Feb 14 14:15:38 mini-pc systemd[1856]: Reached target exit.target - Exit the Session.
Feb 14 14:15:38 mini-pc systemd[1]: user@42.service: Deactivated successfully.
Feb 14 14:15:38 mini-pc systemd[1]: Stopped user@42.service - User Manager for UID 42.
Feb 14 14:15:38 mini-pc audit[1]: SERVICE_STOP pid=1 uid=0 auid=4294967295 ses=4294967295 subj=>
Feb 14 14:15:38 mini-pc systemd[1]: Stopping user-runtime-dir@42.service - User Runtime Directo>
Feb 14 14:15:38 mini-pc systemd[1]: run-user-42.mount: Deactivated successfully.
Feb 14 14:15:38 mini-pc systemd[1]: user-runtime-dir@42.service: Deactivated successfully.
Feb 14 14:15:38 mini-pc systemd[1]: Stopped user-runtime-dir@42.service - User Runtime Director>
Feb 14 14:15:38 mini-pc audit[1]: SERVICE_STOP pid=1 uid=0 auid=4294967295 ses=4294967295 subj=>
Feb 14 14:15:38 mini-pc systemd[1]: Removed slice user-42.slice - User Slice of UID 42.
Feb 14 14:15:38 mini-pc systemd[1]: user-42.slice: Consumed 4.367s CPU time, 659M memory peak.
Feb 14 14:15:38 mini-pc systemd-logind[1302]: Removed session 3.
Feb 14 14:15:39 mini-pc systemd[1]: fprintd.service: Deactivated successfully.
Feb 14 14:15:39 mini-pc audit[1]: SERVICE_STOP pid=1 uid=0 auid=4294967295 ses=4294967295 subj=>
Feb 14 14:15:39 mini-pc audit: BPF prog-id=92 op=UNLOAD
Feb 14 14:15:49 mini-pc systemd[1]: systemd-hostnamed.service: Deactivated successfully.
Feb 14 14:15:49 mini-pc audit[1]: SERVICE_STOP pid=1 uid=0 auid=4294967295 ses=4294967295 subj=>
Feb 14 14:15:49 mini-pc audit: BPF prog-id=86 op=UNLOAD
Feb 14 14:15:52 mini-pc systemd[1]: systemd-timedated.service: Deactivated successfully.
Feb 14 14:15:52 mini-pc audit[1]: SERVICE_STOP pid=1 uid=0 auid=4294967295 ses=4294967295 subj=>
Feb 14 14:15:52 mini-pc audit: BPF prog-id=95 op=UNLOAD
Feb 14 14:15:52 mini-pc audit: BPF prog-id=94 op=UNLOAD
Feb 14 14:15:52 mini-pc audit: BPF prog-id=93 op=UNLOAD
Feb 14 14:15:57 mini-pc com.brave.Browser.desktop[4735]: Fontconfig error: Cannot load default >
Feb 14 14:16:04 mini-pc systemd[1]: systemd-localed.service: Deactivated successfully.
Feb 14 14:16:04 mini-pc audit[1]: SERVICE_SFeb 14 14:16:04 mini-pc audit: BPF prog-id=90 op=UNLOAD
Feb 14 14:16:04 mini-pc audit: BPF prog-id=89 op=UNLOAD
Feb 14 14:16:09 mini-pc geoclue[2719]: Service not used for 60 seconds. Shutting down..
Feb 14 14:16:09 mini-pc systemd[1]: geoclue.service: Deactivated successfully.
Feb 14 14:16:10 mini-pc realmd[2812]: quitting realmd service after timeout
Feb 14 14:16:10 mini-pc realmd[2812]: stopping service
Feb 14 14:16:10 mini-pc systemd[1]: realmd.service: Deactivated successfully.
Feb 14 14:16:50 mini-pc systemd[1855]: app-flatpak-com.brave.Browser-4741.scope: Consumed 12.14>
Feb 14 14:16:50 mini-pc systemd[1855]: app-flatpak-com.brave.Browser-3882.scope: Consumed 10.26>
Feb 14 14:17:06 mini-pc systemd[1]: virtqemud.service: Deactivated successfully.
Feb 14 14:17:06 mini-pc audit[1]: SERVICE_STOP pid=1 uid=0 auid=4294967295 ses=4294967295 subj=>
Feb 14 14:17:13 mini-pc systemd[1855]: Starting grub-boot-success.service - Mark boot as succes>
Feb 14 14:17:13 mini-pc systemd[1855]: Finished grub-boot-success.service - Mark boot as succes>
Feb 14 14:18:59 mini-pc systemd[1855]: Started vte-spawn-786bc622-9542-456b-b4da-c0e67ea3d8c0.s>
Feb 14 14:19:01 mini-pc systemd[1855]: Started vte-spawn-8e4acc04-82fa-440a-af39-15ff9d5bdd57.s>
Feb 14 14:19:03 mini-pc systemd[1855]: Started vte-spawn-030fceab-b867-4286-b84a-c0351b8c99f3.s>
Feb 14 14:19:17 mini-pc cinnamon[3736]: Could not load a pixbuf from icon theme.
                                        This may indicate that pixbuf loaders or the mime datab>
Feb 14 14:19:21 mini-pc systemd[1855]: Started dbus-:1.2-org.gnome.DejaDup@0.service.
TOP pid=1 uid=0 auid=4294967295 ses=4294967295 subj=>
Feb 14 14:16:04 mini-pc audit: BPF prog-id=91 op=UNLOAD
2

Are automatic updates enabled?
Change that to ‘Manual’, exit and stop the packagekit service

sudo systemctl stop packagekit.service
sudo systemctl stop packagekit-offline-update.service

check with systemctl status packagekit.service
should look like this:

$ systemctl status packagekit.service |grep -i active:
     Active: inactive (dead)

$ systemctl status packagekit-offline-update.service |grep -i active:
     Active: inactive (dead)

this should keep you system online and stop the reboots.

please post the output of the last command as preformatted text enclosed in </>

 sudo dnf clean all 
 sudo dnf makecache
 sudo dnf check-update
3

I should’ve been more explicit, I do my updates manually and offline with discover. Perhaps the key line in the journal might be:

Feb 14 14:15:37 mini-pc appimagelauncherd[1939]: Directories to watch disappeared, unintegrating AppImages formerly found in there

as when Fedora fails the file system is not available.

4

appimagelauncher seems to be some 3rd party tool. No idea.

But maybe you should be able to get some more info what’s going on with pkcon. At least you need to prevent the automatic reboots.

sudo pkcon offline-status
sudo pkcon offline-get-prepared
sudo pkcon offline-cancel

sudo pkcon get-updates

Then I would probaby start an update check with dnf instead of pkcon/ packagekit and apply the updates online with dnf upgrade --refresh
Dnf does also support offline-upgrades, but in your system’s current state you probably don’t want to try offline-upgrades yet.

5

Mark, some history…

The Fedora team suggested a while back to start using Discover/offline for updates since it is considered more fail-safe. Discover also suggests Upgrades. This has been working except for three times(2 updates, 1 upgrade). My upgrade to f41 was a real trip. This last update scared me since after about the fifth reboot I lost Grub, it couldn’t find the boot mount. After fumbling around I decided to select the firmware option, did a save and exit and resolved the mount point issue. Next time I might not be so lucky. The symptoms to me look like memory leaks but I don’t have the expertise to figure that out. I think you are right about doing updates/upgrades online until packagekit is more stable.

So, as of right now the system seems to be more stable.

I guess this displays the latest Update. Could of used this command…

sudo pkcon offline-status
Status: Success
Updated kf6-filesystem-6.11.0-1.fc41.x86_64
Updated libreoffice-data-1:24.8.4.2-3.fc41.x86_64
Updated kernel-modules-core-6.12.13-200.fc41.x86_64
Updated kernel-core-6.12.13-200.fc41.x86_64
Updated kernel-modules-6.12.13-200.fc41.x86_64
Updated python3-botocore-1.36.19-1.fc41.noarch
Updated libreoffice-ure-common-1:24.8.4.2-3.fc41.x86_64
Updated libreoffice-ure-1:24.8.4.2-3.fc41.x86_64
Updated libreoffice-opensymbol-fonts-1:24.8.4.2-3.fc41.noarch
Updated libaom-3.11.0-1.fc41.x86_64
Updated libheif-1.19.5-3.fc41.x86_64
Updated kernel-tools-libs-6.12.13-200.fc41.x86_64
Updated javascriptcoregtk6.0-2.46.6-1.fc41.x86_64
Updated double-conversion-3.3.1-1.fc41.x86_64
Updated qt6-qtbase-common-6.8.2-3.fc41.noarch
Updated qt6-qtbase-6.8.2-3.fc41.x86_64
Updated qt6-qtbase-gui-6.8.2-3.fc41.x86_64
Updated kf6-kconfig-6.11.0-1.fc41.x86_64
Updated kf6-kcoreaddons-6.11.0-1.fc41.x86_64
Updated kf6-ki18n-6.11.0-1.fc41.x86_64
Updated kf6-kwidgetsaddons-6.11.0-1.fc41.x86_64
Updated kernel-devel-6.12.13-200.fc41.x86_64
TL;DR

sudo pkcon offline-get-prepared
Command failed: No offline updates have been prepared

Interesting, before I executed any of your suggested commands in you first post, both the packagekit.service daemon and packagekit-offline-update.service were dead.
Now the packagekit.service daemon is alive by default.

sudo dnf check
ima-evm-utils-0:1.5-4.fc40.x86_64
obsoleted by “ima-evm-utils < 1.6” from “ima-evm-utils-libs-0:1.6.2-2.fc41.x86_64”
Check discovered 1 problem(s) in 1 package(s)

sudo dnf distro-sync

Updating and loading repositories:
Repositories loaded.
Package Arch Version Repository Size
Removing dependent packages:
ima-evm-utils x86_64 1.5-4.fc40 fedora 144.9 KiB
Downgrading:
vamp-plugin-sdk x86_64 2.10-1.fc41 fedora 541.6 KiB
replacing vamp-plugin-sdk x86_64 2.10-2.fc40 updates 541.7 KiB

Transaction Summary:
Replacing: 1 package
Removing: 1 package
Downgrading: 1 package

Total size of inbound packages is 178 KiB. Need to download 178 KiB.
After this operation, 145 KiB will be freed (install 542 KiB, remove 687 KiB).
Is this ok [y/N]: y
[1/1] vamp-plugin-sdk-0:2.10-1.fc41.x86_64 100% | 310.6 KiB/s | 178.0 KiB | 00m01s

[1/1] Total 100% | 209.1 KiB/s | 178.0 KiB | 00m01s
Running transaction
[1/5] Verify package files 100% | 333.0 B/s | 1.0 B | 00m00s
[2/5] Prepare transaction 100% | 4.0 B/s | 3.0 B | 00m01s
[3/5] Downgrading vamp-plugin-sdk-0:2.10-1.fc41.x86_64 100% | 31.3 MiB/s | 544.5 KiB | 00m00s
[4/5] Removing ima-evm-utils-0:1.5-4.fc40.x86_64 100% | 2.4 KiB/s | 15.0 B | 00m00s
[5/5] Removing vamp-plugin-sdk-0:2.10-2.fc40.x86_64 100% | 26.0 B/s | 19.0 B | 00m01s
Complete!

I think my system is pretty solid(f41)??

6

Can’t speak for the Fedora team. Fedora 41 introduced dnf5 (libdnf5) and does also support offline upgrades. AFAIK packagekit still use dnf4 (libdnf).

maybe consider to do upgrades with dnf, flatpaks can be upgraded with flatpak update

Does the system still reboot automatically? That was really strange, I would expect the system to stay online after an failed offline-upgrade attempt.

7

@anotheruser Mark, fedora was not auto rebooting, on the 2 occasions that Fedora failed after updates the file system disappeared(thus my conclusion that there is a memory leak). By manually rebooting the file system would temporally work. I have no idea how it got fixed(for now). I keep wondering about flatpak, seems many packages are using it.

What should I do with this?

flatpak update
Looking for updates…


        ID                                      Branch       Op       Remote      Download
 1.     org.fedoraproject.Platform.Locale       f41          u        fedora      < 164.3 MB (partial)
 2.     org.fedoraproject.Platform              f41          u        fedora      < 505.4 MB
 3.     org.gimp.GIMP                           stable       u        fedora       < 69.8 MB
8

It appears by using Software/Discover not everything gets updated(flatpak). By running sudo dnf upgrade --offline most everything gets updated. Hopefully, by using dnf5 directly my issues will be solved.