Garuda-update failed to prepare transation because of libxml2

Elmar · April 30, 2025, 9:38pm

Hi everbody,

I was about to garuda-update my system. But it ran into a problem:

error: failed to prepare transaction (could not satisfy dependencies)
:: unable to satisfy dependency 'libxml2.so=2-64' required by electron33
:: installing libxml2 (2.14.2-2) breaks dependency 'libxml2.so=2-64' required by electron27
:: installing libxml2 (2.14.2-2) breaks dependency 'libxml2.so=2-64' required by electron31
:: installing libxml2 (2.14.2-2) breaks dependency 'libxml2.so=2-64' required by electron32
:: installing libxml2 (2.14.2-2) breaks dependency 'libxml2.so=2-64' required by electron34
:: installing libxml2 (2.14.2-2) breaks dependency 'libxml2.so=2-64' required by electron35
:: installing libelf (0.193-2) breaks dependency 'libelf=0.192' required by lib32-libelf
:: installing libxml2 (2.14.2-2) breaks dependency 'libxml2.so=2-64' required by librest
:: installing libxml2 (2.14.2-2) breaks dependency 'libxml2.so=2-64' required by openconnect
:: installing libxml2 (2.14.2-2) breaks dependency 'libxml2.so=2-64' required by sane

As I just figured out, these electron packages are unused baggage. I just removed them. It seems like, these electron packages quickly become outdated and don’t get removed automatically. I also had an “electron” package which I removed.

The “sane” package is ultimately used by Garuda’s scanner-support and kolourpaint. “lib32-libelf” is for 32-bit support in graphics drivers (lib32-vulkan-radeon, lib32-mesa, lib32-gstreamer). I am not using AMD tech yet, the radeon one could be safe to remove. For the others, I don’t know. “librest” is ultimately required by “virt-viewer” (not sure what it does). “openclient” is ultimately used by Garuda’s “networkmanager-support”.

Do you use alternative packages?

FYI, here is the garuda-inxi

System:
Kernel: 6.14.4-zen1-1-zen arch: x86_64 bits: 64 compiler: gcc v: 14.2.1
clocksource: tsc avail: acpi_pm
parameters: BOOT_IMAGE=/@/boot/vmlinuz-linux-zen
root=UUID=11d26dd1-3904-490b-9e30-1b11c6731dc0 rw rootflags=subvol=@
rd.udev.log_priority=3 vt.global_cursor_default=0 loglevel=3
sysrq_always_enabled=1 ibt=off
Desktop: KDE Plasma v: 6.3.4 tk: Qt v: N/A info: frameworks v: 6.13.0
wm: kwin_wayland vt: 1 dm: SDDM Distro: Garuda base: Arch Linux
Machine:
Type: Detachable System: SHIFT product: SHIFT13mi v: N/A
serial: <superuser required>
Mobo: SHIFT model: SHIFT13mi-pcb v: 06 serial: <superuser required>
part-nu: 0752454247011 uuid: <superuser required> UEFI: American Megatrends
LLC. v: 5.19 date: 01/13/2023
Battery:
ID-1: BAT0 charge: 12.3 Wh (66.5%) condition: 18.5/53.9 Wh (34.3%)
volts: 11.7 min: 11.6 model: Intel SR 1 SR Real Battery type: Unknown
serial: <filter> status: discharging
CPU:
Info: model: 11th Gen Intel Core i5-1135G7 bits: 64 type: MT MCP
arch: Tiger Lake gen: core 11 level: v4 note: check built: 2020
process: Intel 10nm family: 6 model-id: 0x8C (140) stepping: 1
microcode: 0xB8
Topology: cpus: 1x dies: 1 clusters: 4 cores: 4 threads: 8 tpc: 2
smt: enabled cache: L1: 320 KiB desc: d-4x48 KiB; i-4x32 KiB L2: 5 MiB
desc: 4x1.2 MiB L3: 8 MiB desc: 1x8 MiB
Speed (MHz): avg: 400 min/max: 400/4200 scaling: driver: intel_pstate
governor: powersave cores: 1: 400 2: 400 3: 400 4: 400 5: 400 6: 400 7: 400
8: 400 bogomips: 38707
Flags: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
Vulnerabilities: <filter>
Graphics:
Device-1: Intel TigerLake-LP GT2 [Iris Xe Graphics] driver: i915 v: kernel
alternate: xe arch: Xe process: Intel 10nm built: 2020-21 ports:
active: eDP-1 empty: DP-1, DP-2, DP-3, DP-4, DP-5, HDMI-A-1
bus-ID: 00:02.0 chip-ID: 8086:9a49 class-ID: 0300
Device-2: Orbbec 3D USB 2.0 Camera driver: snd-usb-audio,uvcvideo
type: USB rev: 2.0 speed: 480 Mb/s lanes: 1 mode: 2.0 bus-ID: 3-5:2
chip-ID: 2bc5:051e class-ID: 0102 serial: <filter>
Display: wayland server: X.org v: 1.21.1.16 with: Xwayland v: 24.1.6
compositor: kwin_wayland driver: X: loaded: modesetting
alternate: fbdev,intel,vesa dri: iris gpu: i915 display-ID: 0
Monitor-1: eDP-1 model: BOE Display 0x08dd built: 2019 res:
mode: 1920x1080 hz: 60 scale: 100% (1) dpi: 166 gamma: 1.2
size: 294x165mm (11.57x6.5") diag: 337mm (13.3") ratio: 16:9
modes: 1920x1080
API: EGL v: 1.5 hw: drv: intel iris platforms: device: 0 drv: iris
device: 1 drv: swrast gbm: drv: iris surfaceless: drv: iris wayland:
drv: iris x11: drv: iris
API: OpenGL v: 4.6 compat-v: 4.5 vendor: intel mesa v: 25.0.4-arch1.1
glx-v: 1.4 direct-render: yes renderer: Mesa Intel Iris Xe Graphics (TGL
GT2) device-ID: 8086:9a49 memory: 15.18 GiB unified: yes display-ID: :1.0
API: Vulkan v: 1.4.309 layers: 6 device: 0 type: integrated-gpu name: Intel
Iris Xe Graphics (TGL GT2) driver: mesa intel v: 25.0.4-arch1.1
device-ID: 8086:9a49 surfaces: xcb,xlib,wayland device: 1 type: cpu
name: llvmpipe (LLVM 19.1.7 256 bits) driver: mesa llvmpipe
v: 25.0.4-arch1.1 (LLVM 19.1.7) device-ID: 10005:0000
surfaces: xcb,xlib,wayland
Info: Tools: api: clinfo, eglinfo, glxinfo, vulkaninfo
de: kscreen-console,kscreen-doctor wl: wayland-info
x11: xdpyinfo, xprop, xrandr
Audio:
Device-1: Intel Tiger Lake-LP Smart Sound Audio driver: snd_hda_intel
v: kernel alternate: snd_soc_avs,snd_sof_pci_intel_tgl bus-ID: 00:1f.3
chip-ID: 8086:a0c8 class-ID: 0403
Device-2: Orbbec 3D USB 2.0 Camera driver: snd-usb-audio,uvcvideo
type: USB rev: 2.0 speed: 480 Mb/s lanes: 1 mode: 2.0 bus-ID: 3-5:2
chip-ID: 2bc5:051e class-ID: 0102 serial: <filter>
API: ALSA v: k6.14.4-zen1-1-zen status: kernel-api tools: N/A
Server-1: sndiod v: N/A status: off tools: aucat,midicat,sndioctl
Server-2: PipeWire v: 1.4.2 status: active with: 1: pipewire-pulse
status: active 2: wireplumber status: active 3: pipewire-alsa type: plugin
4: pw-jack type: plugin tools: pactl,pw-cat,pw-cli,wpctl
Network:
Device-1: Intel Wi-Fi 6 AX201 driver: iwlwifi v: kernel bus-ID: 00:14.3
chip-ID: 8086:a0f0 class-ID: 0280
IF: wlo1 state: up mac: <filter>
Info: services: NetworkManager, smbd, systemd-timesyncd, wpa_supplicant
Bluetooth:
Device-1: Intel AX201 Bluetooth driver: btusb v: 0.8 type: USB rev: 2.0
speed: 12 Mb/s lanes: 1 mode: 1.1 bus-ID: 3-10:4 chip-ID: 8087:0026
class-ID: e001
Report: btmgmt ID: hci0 rfk-id: 0 state: up address: <filter> bt-v: 5.2
lmp-v: 11 status: discoverable: no pairing: no class-ID: 6c0000
Drives:
Local Storage: total: 953.87 GiB used: 258.29 GiB (27.1%)
SMART Message: Unable to run smartctl. Root privileges required.
ID-1: /dev/nvme0n1 maj-min: 259:0 vendor: Lexar model: SSD NM6A1 1TB
size: 953.87 GiB block-size: physical: 512 B logical: 512 B speed: 31.6 Gb/s
lanes: 4 tech: SSD serial: <filter> fw-rev: V1.25D temp: 42.9 C
scheme: GPT
Partition:
ID-1: / raw-size: 48.14 GiB size: 48.14 GiB (100.00%)
used: 26.13 GiB (54.3%) fs: btrfs dev: /dev/nvme0n1p7 maj-min: 259:6
ID-2: /boot/efi raw-size: 501 MiB size: 500 MiB (99.80%)
used: 612 KiB (0.1%) fs: vfat dev: /dev/nvme0n1p6 maj-min: 259:5
ID-3: /home raw-size: 280.27 GiB size: 280.27 GiB (100.00%)
used: 232.15 GiB (82.8%) fs: btrfs dev: /dev/nvme0n1p8 maj-min: 259:7
ID-4: /var/log raw-size: 48.14 GiB size: 48.14 GiB (100.00%)
used: 26.13 GiB (54.3%) fs: btrfs dev: /dev/nvme0n1p7 maj-min: 259:6
ID-5: /var/tmp raw-size: 48.14 GiB size: 48.14 GiB (100.00%)
used: 26.13 GiB (54.3%) fs: btrfs dev: /dev/nvme0n1p7 maj-min: 259:6
Swap:
Kernel: swappiness: 133 (default 60) cache-pressure: 100 (default) zswap: no
ID-1: swap-1 type: zram size: 31.08 GiB used: 27.3 MiB (0.1%)
priority: 100 comp: zstd avail: lzo-rle,lzo,lz4,lz4hc,deflate,842
max-streams: 8 dev: /dev/zram0
ID-2: swap-2 type: partition size: 3.91 GiB used: 0 KiB (0.0%)
priority: -2 dev: /dev/nvme0n1p9 maj-min: 259:8
Sensors:
System Temperatures: cpu: 34.0 C mobo: N/A
Fan Speeds (rpm): N/A
Info:
Memory: total: 32 GiB note: est. available: 31.08 GiB used: 7.41 GiB (23.8%)
Processes: 323 Power: uptime: 23m states: freeze,mem,disk suspend: s2idle
avail: deep wakeups: 0 hibernate: platform avail: shutdown, reboot,
suspend, test_resume image: 12.41 GiB services: org_kde_powerdevil,
power-profiles-daemon, upowerd Init: systemd v: 257 default: graphical
tool: systemctl
Packages: pm: pacman pkgs: 2493 libs: 578 tools: pamac,paru Compilers:
clang: 19.1.7 gcc: 14.2.1 Shell: garuda-inxi default: Bash v: 5.2.37
running-in: konsole inxi: 3.3.38
Garuda (2.7.2-1):
System install date:     2023-04-30
Last full system update: 2025-04-27
Is partially upgraded:   No
Relevant software:       snapper NetworkManager dracut
Windows dual boot:       Probably (Run as root to verify)
Failed units:

Regards, Elmar.

Elmar · April 30, 2025, 10:00pm

Now I have removed orphaned dependency packages with pacman. Oof, I hope the system will still reboot.

I concocted this command

sudo pacman -Rn $(sudo pacman -Qdt | cut -d' ' -f1 | tr '\n' ' ')

(Actually I forgot the ‘n’ after the -R, but you shouldn’t forget it. It prevents removal of packages which are still required by others, for satefy.)

SGS · April 30, 2025, 10:03pm

Did you search about in forum?
Just use cleanup in terminal.

Elmar · April 30, 2025, 10:06pm

Oh cool, I almost assumed, you guys have such a utility.

Lucky, the ninja command worked out. It reboots and my system garuda-updates again!

Elmar · April 30, 2025, 10:11pm

Oh, the cleanup alias does exactly that but recursively with -Rns instead.

pep · April 30, 2025, 10:21pm

Grüessäch Elmar,
I ran into this same issue rn too, but doing the cleanup thing still spits out:

error: failed to prepare transaction (could not satisfy dependencies)
:: installing libxml2 (2.14.2-2) breaks dependency 'libxml2.so=2-64' required by electron34
:: installing libelf (0.193-2) breaks dependency 'libelf=0.192' required by lib32-libelf
:: installing libxml2 (2.14.2-2) breaks dependency 'libxml2.so=2-64' required by librest
:: installing libxml2 (2.14.2-2) breaks dependency 'libxml2.so=2-64' required by openconnect
:: installing libxml2 (2.14.2-2) breaks dependency 'libxml2.so=2-64' required by sane

Am I missing something?

LG, Pep

dbarron · April 30, 2025, 10:24pm

Just wait (or possibly change mirrors), it’ll sort itself out shortly. Mine cleared about 30 minutes ago.

Elmar · April 30, 2025, 10:46pm

Hey pep,

electron34 was unused on my system. You can check it with

sudo pacman -Qi electron34 | grep -i 'required by'

If so, you can uninstall it to your liking. I couldn’t find it on bauh (under the query “electron”) so I used sudo pacman -Rn electron34 for example.

The other blockers in your error message actually went away on my system after I executed my command. There is a tiny quirks in Garuda’s cleanup which actually shouldn’t affect it’s functionality. It uses sudo pacman -Rns $(sudo pacman -Qdtq) without the cut (version numbers are passed to the pacman remove command). I don’t know what else could help because the cleanup would actually remove all automatically installed packages which became orphans (i.e. are not used anymore).

SGS · April 30, 2025, 10:58pm

We use a better, not so strict one, since some month IIRC.

# Cleanup local orphaned packages
function cleanup
    while pacman -Qdtq
        sudo pacman -R (pacman -Qdtq)
    end
end

system · May 2, 2025, 10:59pm

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