Upgrade to Fedora 43 failed: no graphical interface, duplicate packages,

Hi,

Yesterday evening, I updated my laptop to Fedora 43 using Gnome’s software manager. It gave me no errors except that some nvidia packages would not carry over, which was fine by me, so I went through with the update. That all went fine, but afterwards on boot, I only get a black screen with a text cursor on the top right. I’ve searched and found some threads with similar problems, but those fixes have not worked so far.

These are the issues I’m seeing:

  • gnome-shell crashes and outputs a core dump

  • All my packages are duplicated with a version for Fedora 42 and 43, as seen through dnf repoquery –-duplicates.

  • sudo dnf distro-sync --releasever=43 --refresh outputs:

    
    Updating and loading repositories:
    RPM Fusion for Fedora 43 - Nonfree                                                                                                       100% |   3.8 KiB/s |   9.0 KiB |  00m02s
    RPM Fusion for Fedora 43 - Nonfree - Updates                                                                                             100% |   4.3 KiB/s |   8.3 KiB |  00m02s
    RPM Fusion for Fedora 43 - Nonfree - Steam                                                                                               100% |   4.4 KiB/s |   8.3 KiB |  00m02s
    RPM Fusion for Fedora 43 - Nonfree - NVIDIA Driver                                                                                       100% |   4.7 KiB/s |   8.6 KiB |  00m02s
    RPM Fusion for Fedora 43 - Free - Updates                                                                                                100% |   4.7 KiB/s |   8.2 KiB |  00m02s
    RPM Fusion for Fedora 43 - Free                                                                                                          100% |   6.8 KiB/s |   8.9 KiB |  00m01s
    Fedora 43 - x86_64                                                                                                                       100% |  17.2 KiB/s |  21.0 KiB |  00m01s
    Fedora 43 openh264 (From Cisco) - x86_64                                                                                                 100% |   1.2 KiB/s | 986.0   B |  00m01s
    Fedora 43 - x86_64 - Updates                                                                                                             100% |  19.2 KiB/s |   8.6 KiB |  00m00s
    Repositories loaded.
    Failed to resolve the transaction:
    Problem: The operation would result in removing the following protected packages: NetworkManager, dnf5, gnome-shell, grub2-tools-minimal, selinux-policy-targeted, setup, sudo, systemd, systemd-udev
    You can try to add to command line:
    –skip-broken to skip uninstallable packages
    
  • The kernel for Fedora 43 was not able to be selected. I tried removing and installing it through dnf upgrade, but this failed.

Things I’ve tried:

  • Removing and installing the Nvidia drivers, currently not installed anymore.

  • Distro-sync, as seen above.

  • sudo authselect select local with-silent-lastlog with-fingerprint with-mdns4 --force, which did not change anything as far as I know.

  • /etc/gdm/custom.conf has WaylandEnable=false commented, so not a problem.

  • cat /etc/*-release outputs:

    Fedora release 43 (Forty Three)
    NAME="Fedora Linux"
    VERSION="43 (Workstation Edition)"
    RELEASE_TYPE=stable
    ID=fedora
    VERSION_ID=43
    VERSION_CODENAME=""
    PRETTY_NAME="Fedora Linux 43 (Workstation Edition)"
    ANSI_COLOR="0;38;2;60;110;180"
    LOGO=fedora-logo-icon
    CPE_NAME="cpe:/o:fedoraproject:fedora:43"
    DEFAULT_HOSTNAME="fedora"
    HOME_URL="https://fedoraproject.org/"
    DOCUMENTATION_URL="https://docs.fedoraproject.org/en-US/fedora/f43/"
    SUPPORT_URL="https://ask.fedoraproject.org/"
    BUG_REPORT_URL="https://bugzilla.redhat.com/"
    REDHAT_BUGZILLA_PRODUCT="Fedora"
    REDHAT_BUGZILLA_PRODUCT_VERSION=43
    REDHAT_SUPPORT_PRODUCT="Fedora"
    REDHAT_SUPPORT_PRODUCT_VERSION=43
    SUPPORT_END=2026-12-02
    VARIANT="Workstation Edition"
    VARIANT_ID=workstation
    Fedora release 43 (Forty Three)
    Fedora release 43 (Forty Three)
    
  • systemctl --failed outputs:

      UNIT                                 LOAD   ACTIVE SUB    DESCRIPTION                   
    ● systemd-update-utmp-runlevel.service loaded failed failed Record Runlevel Change in UTMP
    

Some information about my system:

inxi -Fxzz
System:
  Kernel: 6.18.5-100.fc42.x86_64 arch: x86_64 bits: 64 compiler: gcc v: 15.2.1
  Console: pty pts/0 Distro: Fedora Linux 43 (Workstation Edition)
Machine:
  Type: Laptop System: LENOVO product: 20HJS14M00 v: ThinkPad P51 serial: <superuser required>
  Mobo: LENOVO model: 20HJS14M00 serial: <superuser required> Firmware: UEFI vendor: LENOVO
    v: N1UET91W (1.65 ) date: 07/30/2024
Battery:
  ID-1: BAT0 charge: 57.5 Wh (77.2%) condition: 74.5/90 Wh (82.8%) volts: 11.94 min: 11.25
    model: SMP 00NY493 status: not charging
CPU:
  Info: quad core model: Intel Core i7-7700HQ bits: 64 type: MT MCP arch: Kaby Lake rev: 9 cache:
    L1: 256 KiB L2: 1024 KiB L3: 6 MiB
  Speed (MHz): avg: 800 min/max: 800/3800 cores: 1: 800 2: 800 3: 800 4: 800 5: 800 6: 800
    7: 800 8: 800 bogomips: 44798
  Flags-basic: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
Graphics:
  Device-1: Intel Kaby Lake-H GT2 [HD Graphics 630] vendor: Lenovo driver: i915 v: kernel
    arch: Gen-9.5 bus-ID: 00:02.0
  Device-2: NVIDIA GM107GLM [Quadro M1200 Mobile] vendor: Lenovo driver: N/A arch: Maxwell
    bus-ID: 01:00.0
  Device-3: Bison Integrated Camera driver: uvcvideo type: USB bus-ID: 1-8:2
  Display: web server: X.org v: 1.21.1.21 with: Xwayland v: 24.1.9 driver: X:
    loaded: modesetting,nouveau failed: nvidia dri: iris gpu: i915 tty: 178x38 resolution: 1920x1080
  API: OpenGL Message: GL data unavailable in console. Try -G --display
  API: Vulkan v: 1.4.328 drivers: intel,llvmpipe surfaces: N/A devices: 2
  API: EGL Message: EGL data unavailable in console, eglinfo missing.
  Info: Tools: api: glxinfo,vulkaninfo x11: xdriinfo, xdpyinfo, xprop, xrandr
Audio:
  Device-1: Intel CM238 HD Audio vendor: Lenovo driver: snd_hda_intel v: kernel bus-ID: 00:1f.3
  Device-2: NVIDIA GM107 High Definition Audio [GeForce 940MX] driver: snd_hda_intel v: kernel
    bus-ID: 01:00.1
  API: ALSA v: k6.18.5-100.fc42.x86_64 status: kernel-api
  Server-1: PipeWire v: 1.4.10 status: off
Network:
  Device-1: Intel Ethernet I219-V vendor: Lenovo driver: e1000e v: kernel port: N/A
    bus-ID: 00:1f.6
  IF: enp0s31f6 state: down mac: <filter>
  Device-2: Intel Wireless 8265 / 8275 driver: iwlwifi v: kernel bus-ID: 04:00.0
  IF: wlp4s0 state: up mac: <filter>
  IF-ID-1: virbr0 state: down mac: <filter>
  IF-ID-2: virbr1 state: down mac: <filter>
Bluetooth:
  Device-1: Intel Bluetooth wireless interface driver: btusb v: 0.8 type: USB bus-ID: 1-14:4
  Report: btmgmt ID: hci0 rfk-id: 1 state: up address: N/A
Drives:
  Local Storage: total: 1.14 TiB used: 703.46 GiB (60.1%)
  ID-1: /dev/nvme0n1 vendor: Samsung model: SSD 980 1TB size: 931.51 GiB temp: 28.9 C
  ID-2: /dev/nvme1n1 vendor: Samsung model: MZVLW256HEHP-000L7 size: 238.47 GiB temp: 26.9 C
Partition:
  ID-1: / size: 929.93 GiB used: 703 GiB (75.6%) fs: btrfs dev: /dev/nvme0n1p3
  ID-2: /boot size: 973.4 MiB used: 456.8 MiB (46.9%) fs: ext4 dev: /dev/nvme0n1p2
  ID-3: /boot/efi size: 598.8 MiB used: 19.4 MiB (3.2%) fs: vfat dev: /dev/nvme0n1p1
  ID-4: /home size: 929.93 GiB used: 703 GiB (75.6%) fs: btrfs dev: /dev/nvme0n1p3
Swap:
  ID-1: swap-1 type: zram size: 8 GiB used: 0 KiB (0.0%) dev: /dev/zram0
Sensors:
  System Temperatures: cpu: 41.0 C pch: 35.0 C mobo: N/A
  Fan Speeds (rpm): fan-1: 0 fan-2: 0
Info:
  Memory: total: 16 GiB note: est. available: 15.34 GiB used: 1.22 GiB (7.9%)
  target:  UNIT LOAD ACTIVE SUB DESCRIPTION
  Packages: 88 note: see --rpm Compilers: gcc: 15.2.1 Shell: Bash v: 5.3.0 inxi: 3.3.40

Parts of sudo journalctl -b -p err..emerg --no-hostname:

Jan 21 11:12:18 kernel: SELinux: https://github.com/SELinuxProject/selinux-kernel/wiki/DEPRECATE-runtime-disable
Jan 21 11:12:18 kernel: SELinux: Runtime disable is not supported, use selinux=0 on the kernel cmdline.
Jan 21 11:12:18 (sd-exec-[487]: /usr/lib/systemd/system-generators/podman-system-generator failed with exit status 1.
Jan 21 11:12:20 kernel: Bluetooth: hci0: Failed to load Intel firmware file intel/ibt-12-16.sfi (-2)
Jan 21 11:12:20 kernel: Bluetooth: hci0: Reading supported features failed (-56)
Jan 21 11:12:23 abrt-notification[1312]: System encountered a non-fatal error in warn_thunk_thunk()
Jan 21 11:12:29 gdm-launch-environment][1540]: pam_env(gdm-launch-environment:setcred): Unable to read configuration file /etc//environment line 1: Missing delimiter
Jan 21 11:12:29 30-systemd-environment-d-generator[1589]: /usr/lib/environment.d/99-environment.conf:2: invalid variable name "export MESA_LOADER_DRIVER_OVERRIDE", ignoring.
Jan 21 11:12:31 gnome-shell[1637]: Settings schema 'org.gnome.shell.keybindings' does not contain a key named 'screen-brightness-up'
Jan 21 11:12:31 systemd-coredump[1741]: Process 1637 (gnome-shell) of user 60578 dumped core.
Jan 21 11:12:31 systemd[1577]: Failed to start org.gnome.Shell@wayland.service - GNOME Shell on Wayland.
Jan 21 11:12:32 gdm-launch-environment][1540]: pam_env(gdm-launch-environment:setcred): Unable to read configuration file /etc//environment line 1: Missing delimiter
Jan 21 11:12:32 gdm-launch-environment][1817]: pam_env(gdm-launch-environment:setcred): Unable to read configuration file /etc//environment line 1: Missing delimiter
Jan 21 11:12:32 30-systemd-environment-d-generator[1838]: /usr/lib/environment.d/99-environment.conf:2: invalid variable name "export MESA_LOADER_DRIVER_OVERRIDE", ignoring.
Jan 21 11:12:32 systemd-update-utmp[1853]: Unknown command verb 'runlevel'.
Jan 21 11:12:32 systemd[1]: Failed to start systemd-update-utmp-runlevel.service - Record Runlevel Change in UTMP.

Thanks in advance for helping!

Repos seem to all be out of date after upgrading to 43 - #4 by vgaetera

1 Like

This fixed it! Thank you so much.

1 Like