GNOME flickers and unresponsiveness after an upgrade to kernel Version 6.17.8

[juancnuno]

I am new to NixOS as of October 18. This is my first post in this discourse.

I have gotten into a regular, daily upgrade routine. This morning my upgrade had significant issues and I had to roll back to my previous system generation. This is the first time that’s happened for me. I noticed that my kernel went from 6.17.7 to 6.17.8 between generations. When I rebooted after the upgrade edges of my Text Editor would start flickering and some operations (hamburger menu - About Text Editor) would become unresponsive. I’ve been able to use the mouse and the GNOME menu in the upper right corner to reboot.

I figure folks here would like to know this. I do not use flakes; I use channels. Here are my system channels:

[juancnuno@usscerritos:~]$ sudo nix-channel --list
[sudo] password for juancnuno: 
nixos https://channels.nixos.org/nixos-unstable
nixos-hardware https://github.com/NixOS/nixos-hardware/archive/master.tar.gz

Here is my configuration. My laptop is a Framework 13 with a 12th Gen Intel Core that I normally keep closed and plugged into a desktop monitor connected via USB-C. I use a desktop keyboard and mouse connected to the monitor.

For now I’ll stick to the good generation and try to roll forward when I notice a kernel after 6.17.8. I’m operating on hunches here

[juancnuno]

It occurred to me to take a peek at my journalctl

[juancnuno@usscerritos:~]$ journalctl -b -7 -p 4

Nov 17 05:21:44 usscerritos org.gnome.TextEditor[3156]: MESA-INTEL: warning: ../src/intel/vulkan/anv_formats.c:993: FINISHME: support more multi-planar formats with DRM modifiers
Nov 17 05:21:44 usscerritos org.gnome.TextEditor[3156]: MESA-INTEL: warning: ../src/intel/vulkan/anv_formats.c:959: FINISHME: support YUV colorspace with DRM format modifiers
Nov 17 05:21:46 usscerritos gsd-datetime[2301]: g_ascii_strtod: assertion 'nptr != NULL' failed
Nov 17 05:21:48 usscerritos org.gnome.Console[3276]: MESA-INTEL: warning: ../src/intel/vulkan/anv_formats.c:993: FINISHME: support more multi-planar formats with DRM modifiers
Nov 17 05:21:48 usscerritos org.gnome.Console[3276]: MESA-INTEL: warning: ../src/intel/vulkan/anv_formats.c:959: FINISHME: support YUV colorspace with DRM format modifiers
Nov 17 05:21:57 usscerritos ModemManager[2064]: <wrn> [plugin/generic] could not grab port ttyS0: Cannot add port 'tty/ttyS0', unhandled port type
Nov 17 05:21:57 usscerritos ModemManager[2064]: <wrn> [base-manager] couldn't create modem for device '/sys/devices/pci0000:00/0000:00:16.3': Failed to find primary AT port
Nov 17 05:22:25 usscerritos localsearch-3[2448]: Could not ask extractor to update: GDBus.Error:org.freedesktop.DBus.Error.UnknownMethod: Object does not exist at path “/org/freedesktop/Tracker3/Extract”
Nov 17 05:22:25 usscerritos localsearch-3[2448]: Could not ask extractor to update: GDBus.Error:org.freedesktop.DBus.Error.UnknownMethod: Object does not exist at path “/org/freedesktop/Tracker3/Extract”
Nov 17 05:23:52 usscerritos kgx[3276]: Vulkan: ../src/intel/vulkan/i915/anv_device.c:349: GPU hung on one of our command buffers (VK_ERROR_DEVICE_LOST)
Nov 17 05:23:52 usscerritos kgx[3276]: vkWaitForFences(): The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 17 05:23:52 usscerritos kgx[3276]: vkQueueSubmit(): The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 17 05:23:52 usscerritos kgx[3276]: vkQueuePresentKHR(): The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 17 05:24:16 usscerritos org.gnome.Nautilus[7339]: Localsearch search engine has no connection
Nov 17 05:24:16 usscerritos org.gnome.Characters[7343]: MESA-INTEL: warning: ../src/intel/vulkan/anv_formats.c:993: FINISHME: support more multi-planar formats with DRM modifiers
Nov 17 05:24:16 usscerritos org.gnome.Characters[7343]: MESA-INTEL: warning: ../src/intel/vulkan/anv_formats.c:959: FINISHME: support YUV colorspace with DRM format modifiers
Nov 17 05:24:28 usscerritos org.freedesktop.secrets[2758]: discover_other_daemon: 1
Nov 17 05:24:28 usscerritos gdm[1453]: Gdm: Failed to list cached users: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name :1.9 was not provided by any .service files
Nov 17 05:24:28 usscerritos localsearch-3[2448]: Owner of volume monitor org.gtk.vfs.AfcVolumeMonitor disconnected from the bus; removing drives/volumes/mounts
Nov 17 05:24:28 usscerritos localsearch-3[2448]: Owner of volume monitor org.gtk.vfs.GoaVolumeMonitor disconnected from the bus; removing drives/volumes/mounts
Nov 17 05:24:28 usscerritos localsearch-3[2448]: Owner of volume monitor org.gtk.vfs.GPhoto2VolumeMonitor disconnected from the bus; removing drives/volumes/mounts
Nov 17 05:24:28 usscerritos localsearch-3[2448]: Owner of volume monitor org.gtk.vfs.MTPVolumeMonitor disconnected from the bus; removing drives/volumes/mounts
Nov 17 05:24:28 usscerritos localsearch-3[2448]: Owner of volume monitor org.gtk.vfs.UDisks2VolumeMonitor disconnected from the bus; removing drives/volumes/mounts
Nov 17 05:24:28 usscerritos pipewire[2476]: mod.x11-bell: X11 I/O error handler called on display :0
Nov 17 05:24:28 usscerritos pipewire[2476]: mod.x11-bell: X11 display (:0) has encountered a fatal I/O error
Nov 17 05:24:28 usscerritos systemd[1]: display-manager.service: Failed with result 'exit-code'.
Nov 17 05:24:28 usscerritos systemd[1]: display-manager.service: Failed to enqueue OnFailure=plymouth-quit.service job, ignoring: Unit plymouth-quit.service not found.
Nov 17 05:24:28 usscerritos gnome-shell[2177]: Connection to xwayland lost
Nov 17 05:24:28 usscerritos gnome-shell[2177]: Owner of volume monitor org.gtk.vfs.AfcVolumeMonitor disconnected from the bus; removing drives/volumes/mounts
Nov 17 05:24:28 usscerritos gnome-shell[2177]: Owner of volume monitor org.gtk.vfs.GoaVolumeMonitor disconnected from the bus; removing drives/volumes/mounts
Nov 17 05:24:28 usscerritos gnome-shell[2177]: Owner of volume monitor org.gtk.vfs.GPhoto2VolumeMonitor disconnected from the bus; removing drives/volumes/mounts
Nov 17 05:24:28 usscerritos gnome-shell[2177]: Owner of volume monitor org.gtk.vfs.MTPVolumeMonitor disconnected from the bus; removing drives/volumes/mounts
Nov 17 05:24:28 usscerritos gnome-shell[2177]: Owner of volume monitor org.gtk.vfs.UDisks2VolumeMonitor disconnected from the bus; removing drives/volumes/mounts
Nov 17 05:24:28 usscerritos gnome-shell[2177]: Error checking authorization for action id org.freedesktop.bolt.enroll: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name :1.13 was not provided by any .service files
Nov 17 05:24:28 usscerritos gnome-shell[2177]: g_hash_table_iter_next: assertion 'ri->version == ri->hash_table->version' failed
Nov 17 05:24:28 usscerritos systemd[1]: sys-devices-pci0000:00-0000:00:1f.3-sound-card1-controlC1.device: Failed to enqueue SYSTEMD_WANTS job, ignoring: Transaction for sound.target/start is destructive (shutdown.target has 'start' job queued, but 'stop' is included in transaction).
Nov 17 05:24:28 usscerritos systemd[1]: sys-devices-virtual-misc-rfkill.device: Failed to enqueue SYSTEMD_WANTS job, ignoring: Transaction for systemd-rfkill.socket/start is destructive (shutdown.target has 'start' job queued, but 'stop' is included in transaction).
Nov 17 05:24:28 usscerritos systemd[1]: sys-devices-pci0000:00-0000:00:14.0-usb3-3\x2d5-3\x2d5.1-3\x2d5.1:1.2-sound-card0-controlC0.device: Failed to enqueue SYSTEMD_WANTS job, ignoring: Transaction for sound.target/start is destructive (shutdown.target has 'start' job queued, but 'stop' is included in transaction).
Nov 17 05:24:28 usscerritos gnome-shell[2177]: Error checking authorization for action id org.freedesktop.NetworkManager.network-control: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name :1.13 was not provided by any .service files
Nov 17 05:24:28 usscerritos gnome-shell[2177]: Could not issue 'GetUnit' systemd call
Nov 17 05:24:28 usscerritos gnome-shell[2177]: Object St.Icon (0x55c1578ae6f0), has been already disposed — impossible to set any property on it. This might be caused by the object having been destroyed from C code using something such as destroy(), dispose(), or remove() vfuncs.
                                               == Stack trace for context 0x55c155265ae0 ==
                                               #0   55c1553574f8 i   resource:///org/gnome/shell/ui/status/bluetooth.js:464 (978f0bed1f0 @ 183)
                                               #1   55c155357478 i   resource:///org/gnome/shell/ui/status/bluetooth.js:449 (978f0bed1a0 @ 12)
                                               #2   55c1553573e8 i   resource:///org/gnome/shell/ui/status/bluetooth.js:62 (978f0bec150 @ 96)
                                               #3   55c155357348 i   resource:///org/gnome/shell/ui/main.js:279 (202367c0d0b0 @ 119)
Nov 17 05:24:28 usscerritos gnome-shell-calendar-server[2250]: The calendar backend for 'Birthdays & Anniversaries' has crashed.
Nov 17 05:24:28 usscerritos gnome-shell-calendar-server[2250]: The calendar backend for 'Personal' has crashed.
Nov 17 05:24:28 usscerritos NetworkManager[1364]: <warn>  [1763385868.7582] dispatcher: (10) failed (after 0.001 sec): Refusing activation, D-Bus is shutting down.
Nov 17 05:24:29 usscerritos kernel: watchdog: watchdog0: watchdog did not stop!

[trespaul]

I think I’m having the exact same problem. I also get a bunch of flickering and / or entirely unresponsive apps, all of which are Gnome or Gnome-native apps, including Settings, Files (Nautilus), Showtime, Celluloid, Amberol, Calendar, Image Viewer, etc., nearly every Gnome app. I even saw a problem with Ghostty’s Gnome-native tab bar glitching one time.

So that makes me think that it’s because of the upgrade to Gnome 49, and also because these issues started exactly after I built and activated the config which updated to Gnome 49.

Launching Nautilus results in, e.g.,

Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkQueueSubmit():     The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkGetFenceStatus():  The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkQueueSubmit():     The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkGetFenceStatus():  The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkGetFenceStatus():  The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkQueueSubmit():     The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkGetFenceStatus():  The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkGetFenceStatus():  The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkGetFenceStatus():  The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkQueueSubmit():     The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkGetFenceStatus():  The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkGetFenceStatus():  The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkGetFenceStatus():  The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkGetFenceStatus():  The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkWaitForFences():   The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkWaitForFences():   The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkQueueSubmit():     The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:09:50 org.gnome.Nautilus[670055]: vkQueuePresentKHR(): The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:10:16 org.gnome.Nautilus[670055]: vkGetFenceStatus():  The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)
Nov 18 20:10:16 org.gnome.Nautilus[670055]: vkWaitForFences():   The logical or physical device has been lost. (VK_ERROR_DEVICE_LOST) (-4)

in journalctl -p4. I assume VK means something to do with Vulkan.

[trespaul]

The update was quite large.

Diff given by nix run nixpkgs#dix -- /nix/store/5a7rqhkdfnjw1rzbzrzn8pf2q7pf6i9b-nixos-system-paulpad-25.11.20251111.9da7f1c/ /nix/store/2fmlrjl1vwnpxv1cwj3p0zlf0zjbzd7w-nixos-system-paulpad-25.11.20251116.50a96ed:

<<< /nix/store/5a7rqhkdfnjw1rzbzrzn8pf2q7pf6i9b-nixos-system-paulpad-25.11.20251111.9da7f1c/
>>> /nix/store/2fmlrjl1vwnpxv1cwj3p0zlf0zjbzd7w-nixos-system-paulpad-25.11.20251116.50a96ed

CHANGED
[U.] adwaita-fonts                               48.2 -> 49.0
[U*] adwaita-icon-theme                          48.0 -> 49.0
[U*] at-spi2-core                                2.56.2 -> 2.58.0
[U.] atomic-counter                              0.1.2.3, 0.1.2.3-doc -> 0.1.2.4, 0.1.2.4-doc
[U.] atuin                                       18.8.0 -> 18.10.0
[U*] baobab                                      48.0 -> 49.0
[U.] bash-completion                             2.16.0 -> 2.17.0
[U.] btrfs-progs                                 6.17 -> 6.17.1
[U.] c-ares                                      1.34.5 -> 1.34.5 ×3
[U.] cabal-add                                   0.1, 0.1-doc -> 0.2, 0.2-doc
[U*] cpupower                                    6.12.57 -> 6.12.58
[U.] dash                                        0.5.12 -> 0.5.13.1
[U*] decibels                                    48.0 -> 49.0
[U.] dialect                                     2.5.0 -> 2.6.1
[U.] dotnet-runtime                              8.0.21 -> 8.0.22
[U.] dotnet-runtime-wrapped                      8.0.21 -> 8.0.22
[U.] electron                                    37.9.0, 38.6.0 -> 37.10.0, 38.7.0
[U.] electron-unwrapped                          37.9.0, 38.6.0 -> 37.10.0, 38.7.0
[U.] elfutils                                    0.193 ×2, 0.193-bin, 0.193-dev -> 0.194 ×2, 0.194-bin, 0.194-dev
[U*] epiphany                                    48.5 -> 49.1
[U.] evolution-data-server                       3.56.2 ×2 -> 3.58.1 ×2
[U.] extensions                                  0.1.0.3, 0.1.0.3-doc -> 0.1.1.0, 0.1.1.0-doc
[U.] ffmpeg                                      6.1.2-data, 6.1.2-lib, 7.1.1-bin, 7.1.1-data, 7.1.1-lib, 7.1.1-man -> 6.1.3-data, 6.1.3-lib, 8.0-bin, 7.1.2-data, 7.1.2-lib, 8.0-man, 8.0-data, 8.0-lib
[U.] ffmpeg-headless                             7.1.1-bin, 7.1.1-data ×2, 7.1.1-lib ×2 -> 8.0-bin, 8.0-data ×2, 8.0-lib ×2
[U*] file-roller                                 44.5 -> 44.6
[U.] fluidsynth                                  2.4.8 -> 2.5.0
[U.] fmt                                         11.2.0 -> 12.0.0
[U.] fourmolu                                    0.19.0.0, 0.19.0.0-doc -> 0.19.0.1, 0.19.0.1-doc
[U.] fractal                                     12.1 -> 13
[U.] gdk-pixbuf                                  2.42.12 -> 2.44.3
[U*] gdm                                         48.0 -> 49.1
[U.] gh                                          2.83.0 -> 2.83.1
[U.] ghcide                                      2.11.0.0, 2.11.0.0-doc -> 2.12.0.0, 2.12.0.0-doc
[U*] git                                         2.51.0, 2.51.0-doc -> 2.51.2, 2.51.2-doc
[U.] gjs                                         1.84.2 -> 1.86.0
[U*] glib                                        2.84.4 ×2, 2.84.4-bin, 2.84.4-dev -> 2.86.1 ×2, 2.86.1-bin, 2.86.1-dev
[U.] glibmm                                      2.84.0 -> 2.86.0
[U.] glycin-loaders                              1.2.3 -> 2.0.5
[U*] gnome-backgrounds                           48.2.1 -> 49.0
[U*] gnome-calculator                            48.1 -> 49.1.1
[U*] gnome-calendar                              48.1 -> 49.0.1
[U*] gnome-characters                            48.0 -> 49.1
[U*] gnome-clocks                                48.0 -> 49.0
[U*] gnome-connections                           48.0 -> 49.0
[U*] gnome-console                               48.0.1 -> 49.1
[U*] gnome-contacts                              48.0 -> 49.0
[U*] gnome-control-center                        48.4 -> 49.1
[U.] gnome-decoder                               0.7.1 -> 0.8.0
[U.] gnome-desktop                               44.3 -> 44.4
[U*] gnome-font-viewer                           48.0 -> 49.0
[U*] gnome-initial-setup                         48.1 -> 49.0
[U*] gnome-logs                                  45.0 -> 49.0
[U*] gnome-maps                                  48.6 -> 49.2
[U*] gnome-music                                 48.1 -> 49.1
[U*] gnome-online-accounts                       3.54.5, 3.54.5-man -> 3.56.1, 3.56.1-man
[U*] gnome-remote-desktop                        48.1 -> 49.1
[U*] gnome-session                               48.0, 48.0-sessions -> 49.1, 49.1-sessions
[U.] gnome-session-ctl                           47.0.1 -> 49.0
[U*] gnome-settings-daemon                       48.1, 48.1-gsettings-schemas -> 49.1, 49.1-gsettings-schemas
[U*] gnome-shell                                 48.4 -> 49.1
[U.] gnome-shell-extensions                      48.3 -> 49.0
[U*] gnome-software                              48.4 -> 49.1
[U*] gnome-system-monitor                        48.1 -> 49.1
[U*] gnome-text-editor                           48.3 -> 49.0
[U*] gnome-tour                                  48.1 -> 49.0
[U.] gnome-tweaks                                46.1 -> 49.0
[U*] gnome-user-docs                             48.2 -> 49.1
[U*] gnome-weather                               48.0 -> 49.0
[U.] gobject-introspection                       1.84.0, 1.84.0-dev -> 1.86.0, 1.86.0-dev
[U.] gobject-introspection-wrapped               1.84.0, 1.84.0-dev -> 1.86.0, 1.86.0-dev
[U.] gom                                         0.5.3 -> 0.5.5
[U.] gsettings-desktop-schemas                   48.0 -> 49.0
[U*] gtk+3                                       3.24.49 -> 3.24.51
[U.] gtk-frdp                                    0-unstable-2025-03-14 -> 0-unstable-2025-08-15
[U.] gtk4                                        4.18.6 -> 4.20.2
[U.] gtkmm                                       4.18.0 -> 4.20.0
[U.] gtksourceview                               5.16.0 -> 5.18.0
[U*] gvfs                                        1.57.2 ×2 -> 1.58.0 ×2
[U.] haskell-language-server                     2.11.0.0 ×2 -> 2.12.0.0 ×2
[U.] hiedb                                       0.6.0.2, 0.6.0.2-doc -> 0.7.0.0, 0.7.0.0-doc
[U.] hls-graph                                   2.11.0.0, 2.11.0.0-data, 2.11.0.0-doc -> 2.12.0.0, 2.12.0.0-data, 2.12.0.0-doc
[U.] hls-plugin-api                              2.11.0.0, 2.11.0.0-doc -> 2.12.0.0, 2.12.0.0-doc
[U.] hls-test-utils                              2.11.0.0, 2.11.0.0-doc -> 2.12.0.0, 2.12.0.0-doc
[U.] icu4c                                       75.1 -> 77.1
[U.] inih                                        61 -> 62
[U.] initrd-linux                                6.12.57 -> 6.12.58
[U.] ipxe                                        1.21.1-unstable-2025-11-05 -> 1.21.1-unstable-2025-11-13
[U.] karchive                                    6.19.0 -> 6.20.0
[U.] kcoreaddons                                 6.19.0 -> 6.20.0
[U*] kexec-tools                                 2.0.31 ×2 -> 2.0.32 ×2
[U.] kimageformats                               6.19.0 -> 6.20.0
[U.] libadwaita                                  1.7.6 -> 1.8.0
[U.] libarchive                                  3.8.1-lib ×2 -> 3.8.2-lib ×2
[U.] libdecor                                    0.2.3 -> 0.2.4
[U.] libdisplay-info                             0.3.0 -> 0.3.0 ×2
[U.] libdrm                                      2.4.126 ×2, 2.4.126-bin ×2, 2.4.126-dev ×2 -> 2.4.127 ×2, 2.4.127-bin ×2, 2.4.127-dev ×2
[U.] libedit                                     20250104-3.1 ×2 -> 20251016-3.1 ×2
[U.] libinput                                    1.29.1 -> 1.29.2
[U.] libpeas                                     2.0.7 -> 2.2.0
[U.] libpq                                       18.0 -> 18.1
[U.] librsvg                                     2.61.1 -> 2.61.2
[U.] libshumate                                  1.4.0 -> 1.5.1
[U.] libtraceevent                               1.8.4 -> 1.8.5
[D.] libunistring                                1.4 ×2 -> 1.4.1 ×2
[U.] libxml2                                     2.15.0 ×3, 2.15.0-bin ×2, 2.15.0-dev, 2.15.0-py -> 2.15.1 ×3, 2.15.1-bin ×2, 2.15.1-dev, 2.15.1-py
[U.] linux                                       6.12.57, 6.12.57-modules ×2, 6.12.57-modules-shrunk -> 6.12.58, 6.12.58-modules ×2, 6.12.58-modules-shrunk
[U.] linux-firmware                              20251021-zstd -> 20251111-zstd
[U*] localsearch                                 3.9.0 -> 3.10.1
[U*] loupe                                       48.1 -> 49.1
[U.] mdns-scanner                                0.25.0 -> 0.25.1
[U.] mesa                                        25.2.6 ×2 -> 25.3.0 ×2
[U.] mupdf                                       1.26.8 ×2, 1.26.8-bin ×2 -> 1.26.10 ×2, 1.26.10-bin ×2
[U.] mutter                                      48.4 -> 49.1.1
[U*] nautilus                                    48.3 -> 49.1
[U.] netavark                                    1.16.1 -> 1.17.0
[U*] networkmanager                              1.52.1 ×2, 1.52.1-doc, 1.52.1-man -> 1.54.1 ×2, 1.54.1-doc, 1.54.1-man
[U.] nixos-system-paulpad                        25.11.20251111.9da7f1c -> 25.11.20251116.50a96ed
[U.] nodejs                                      22.20.0 -> 22.21.1
[U.] onetbb                                      2022.2.0 -> 2022.3.0
[U.] openjdk                                     21.0.9+8 -> 21.0.9+10
[U.] openjdk-headless                            21.0.9+8 -> 21.0.9+10
[U.] openjdk-headless-minimal-jre                21.0.9+8 -> 21.0.9+10
[U.] openjdk-minimal-jre                         21.0.9+8 -> 21.0.9+10
[U.] openjpeg                                    2.5.2 ×2 -> 2.5.4 ×2
[U*] openssh                                     10.1p1 -> 10.2p1, 10.2p1-man
[U*] orca                                        48.6 -> 49.4
[U.] ormolu                                      0.8.0.1, 0.8.0.1-bin, 0.8.0.1-doc -> 0.8.0.2, 0.8.0.2-bin, 0.8.0.2-doc
[U.] p11-kit                                     0.25.9 ×2, 0.25.9-bin -> 0.25.10 ×2, 0.25.10-bin
[U.] pango                                       1.56.4 ×2 -> 1.57.0 ×2
[U+] papers                                      48.5 -> 49.1
[U*] podman                                      5.6.2, 5.6.2-man -> 5.7.0, 5.7.0-man
[U*] podman-docker-compat                        5.6.2 -> 5.7.0
[U.] pretty-simple                               4.1.3.0, 4.1.3.0-doc -> 4.1.4.0, 4.1.4.0-doc
[U.] protobuf                                    32.1 -> 33.0
[U.] publicsuffix-list                           0-unstable-2025-08-28 ×2 -> 0-unstable-2025-10-08 ×2
[U.] python3                                     3.13.8 ×2, 3.13.8-env ×12 -> 3.13.9 ×2, 3.13.9-env ×12
[U.] python3.13-cryptography                     46.0.1 -> 46.0.2
[U.] python3.13-filelock                         3.18.0 -> 3.20.0
[U.] python3.13-icalendar                        6.3.1 -> 6.3.2
[U.] python3.13-idna                             3.10 -> 3.11
[U.] python3.13-numpy                            2.3.3 -> 2.3.4
[U.] python3.13-ocrmypdf                         16.11.1 -> 16.12.0
[U.] python3.13-pikepdf                          9.11.0 -> 10.0.0
[U.] python3.13-pillow                           11.3.0 -> 12.0.0
[U.] python3.13-protobuf                         6.32.1 -> 6.33.0
[U.] python3.13-psutil                           7.1.0 -> 7.1.2
[U.] python3.13-pygobject                        3.50.0, 3.50.0-dev -> 3.54.3, 3.54.3-dev
[U.] python3.13-pynacl                           1.5.0 -> 1.6.0
[U.] python3.13-simplejson                       3.20.1 -> 3.20.2
[U.] python3.13-xmltodict                        0.14.2 -> 1.0.2
[U.] qpdf                                        11.10.1-lib -> 12.2.0-lib
[U.] qtbase                                      5.15.17, 5.15.17-bin -> 5.15.18, 5.15.18-bin
[U.] qtdeclarative                               5.15.17, 5.15.17-bin -> 5.15.18, 5.15.18-bin
[U.] qtquickcontrols                             5.15.17 -> 5.15.18
[U.] qtsvg                                       5.15.17, 5.15.17-bin -> 5.15.18, 5.15.18-bin
[U.] qttools                                     5.15.17, 5.15.17-bin -> 5.15.18, 5.15.18-bin
[U.] qttranslations                              5.15.17 -> 5.15.18
[U.] qtwayland                                   5.15.17, 5.15.17-bin -> 5.15.18, 5.15.18-bin
[U.] qtwebchannel                                5.15.17 -> 5.15.18
[U.] qtwebsockets                                5.15.17, 5.15.17-bin -> 5.15.18, 5.15.18-bin
[U.] regex-tdfa                                  1.3.2.4, 1.3.2.4-doc -> 1.3.2.5, 1.3.2.5-doc
[U.] ruby                                        3.3.9 -> 3.3.10
[U*] rygel                                       0.44.2 -> 45.0
[U.] s2n-tls                                     1.5.26 -> 1.5.27
[U.] sdl2-compat                                 2.32.56 -> 2.32.58
[U.] sdl3                                        3.2.24-lib -> 3.2.26-lib
[U+] showtime                                    48.1 -> 49.0
[U.] signal-desktop-bin                          7.77.1 -> 7.79.0
[U*] simple-scan                                 48.1 -> 49.1
[U*] snapshot                                    48.0.1 -> 49.0
[U.] spidermonkey                                128.14.0 -> 140.4.0
[U*] sudo-rs                                     0.2.9 -> 0.2.10
[C*] systemd                                     258 ×2, 258-man -> 258.1 ×2, 258.1-man
[D.] systemd-minimal                             258 ×2 -> 258.1 ×2
[D.] systemd-minimal-libs                        258 ×2 -> 258.1 ×2
[U*] tailscale                                   1.88.4 -> 1.90.6
[U.] tealdeer                                    1.8.0 -> 1.8.1
[U.] tecla                                       48.0.2 -> 49.0
[U*] tinysparql                                  3.9.2 -> 3.10.1
[U.] tuba                                        0.10.1 -> 0.10.3
[U.] unbound                                     1.24.0-lib ×2 -> 1.24.1-lib ×2
[U.] unordered-containers                        0.2.20, 0.2.20-doc -> 0.2.20.1, 0.2.20.1-doc
[U.] v4l-utils                                   1.30.1 ×2 -> 1.32.0 ×2
[U.] v4l2loopback                                0.15.1-6.12.57, 0.15.1-6.12.57-bin -> 0.15.1-6.12.58, 0.15.1-6.12.58-bin
[U.] vte                                         0.80.3 ×3 -> 0.82.1 ×2
[U*] xdg-desktop-portal-gnome                    48.0 -> 49.0
[U.] xen                                         4.20.1 -> 4.20.2
[U.] xjadeo                                      0.8.14 -> 0.8.15
[U.] xorg-server                                 21.1.18 -> 21.1.20
[U*] yelp                                        42.3 -> 49.0
[U.] yelp-xsl                                    42.4 -> 49.0
[U.] yq-go                                       4.48.1 -> 4.48.2
[U.] zen-browser                                 1.17.6b -> 1.17.7b
[U.] zenity                                      4.1.90 -> 4.2.1

ADDED
[A.] base64-bytestring                           1.2.1.0, 1.2.1.0-doc
[A.] cpphs                                       1.20.10, 1.20.10-doc
[A.] deriving-aeson                              0.2.10, 0.2.10-doc
[A.] double-conversion                           3.3.1-dev
[A.] haskell-src-exts                            1.23.1, 1.23.1-doc
[A.] haskell-src-meta                            0.8.15, 0.8.15-doc
[A.] hlint                                       3.10, 3.10-data, 3.10-doc
[A.] hscolour                                    1.25, 1.25-data, 1.25-doc
[A.] initrd-bin-env                              <none>
[A.] initrd-shells                               <none>
[A.] lcms2                                       2.17-bin, 2.17-dev
[A.] libglycin                                   2.0.5
[A.] libseccomp                                  2.6.0, 2.6.0-dev
[A.] openapv                                     0.2.0.4 ×2
[A.] perl5.40.0-Archive-Zip                      1.68
[A.] perl5.40.0-Compress-Raw-Bzip2               2.206
[A.] perl5.40.0-Compress-Raw-Lzma                2.206
[A.] perl5.40.0-Compress-Raw-Zlib                2.206
[A.] perl5.40.0-Getopt-Long                      2.58
[A.] perl5.40.0-IO-Compress                      2.206
[A.] perl5.40.0-IO-Compress-Brotli               0.019
[A.] perl5.40.0-SUPER                            1.20190531
[A.] perl5.40.0-Test-MockModule                  0.177.0
[A.] polyparse                                   1.13.1, 1.13.1-doc
[A.] python3.13-dasbus-unstable                  11-10-2022
[A.] refact                                      0.3.0.2, 0.3.0.2-doc
[A.] string-interpolate                          0.3.4.0, 0.3.4.0-doc
[A.] text-conversions                            0.3.1.1, 0.3.1.1-doc
[A.] th-expand-syns                              0.4.12.0, 0.4.12.0-doc
[A.] th-lift                                     0.8.6, 0.8.6-doc
[A.] th-orphans                                  0.13.16, 0.13.16-doc
[A.] th-reify-many                               0.1.10, 0.1.10-doc
[A.] unit-graphical-session-pre.target           <none>
[A.] unit-orca.service                           <none>

REMOVED
[R.] initrd-fstab                                <none>
[R.] initrd-units                                <none>
[R.] libportal-gtk3                              0.9.1
[R.] lingering-users                             <none>
[R.] neat-interpolation                          0.5.1.4, 0.5.1.4-doc
[R.] nixos-init                                  0.1.0
[R-] totem                                       43.2
[R.] unit-initrd-find-nixos-closure.service      <none>
[R.] unit-initrd-nixos-activation.service        <none>
[R.] unit-initrd-nixos-copy-secrets.service      <none>
[R.] unit-initrd-parse-etc.service               <none>
[R.] unit-initrd-switch-root.service             <none>
[R.] unit-initrd.target                          <none>
[R.] unit-panic-on-fail.service                  <none>
[R.] unit-script-initrd-find-nixos-closure-start <none>
[R.] unit-script-initrd-nixos-activation-start   <none>
[R.] unit-script-initrd-nixos-copy-secrets-start <none>
[R.] unit-sysroot-run.mount                      <none>
[R.] unit-systemd-tmpfiles-setup-sysroot.service <none>

SIZE: 38.3 GiB -> 38.8 GiB
DIFF: 487 MiB

Really the only big changes that I can see are the kernel and Gnome updates.

[juancnuno]

I tried rolling back to a 6.12 kernel and that didn’t help. I’m in the process of investigating my graphics settings.

[trespaul]

Rolling back Gnome 48←49 and kernel 6.12.57←6.12.58 was successful for me, for what it’s worth.

[juancnuno]

This may be a relevant bug

[theEmeraldM]

I have the same issue on my Framework 12, but not on my home PC running a very similar setup. The main difference that I can think of is that my home PC has an Nvidia GPU, whereas the Framework 12 doesn’t.

After some more looking around, it seems like this is a Mesa 25.3.0 issue, as described in this github issue: nixos/nautilus: artifacts and crash after update to mesa 25.3.0, also affects other GTK4 applications · Issue #463220 · NixOS/nixpkgs · GitHub. I tried the workaround that they suggested, and can confirm that it works on the Framework 12!

[juancnuno]

@theEmeraldM pointed me at the problematic PR. I worked around it with my very first overlay. I have no idea what I’m doing

[juancnuno]

This looks to be the real fix. I rolled my overlay back and things seem stable.