Boot error: Failed to start D-Bus System Message Bus

I encounter problems during boot, i.e.

[FAILED] Failed to start D-Bus System Message Bus

I could not really assign the issue to recent changes.

Therefore I conducted the following steps:

  1. chroot
  2. reinstall with pacman -SYu, but failed

I found many packages being corrupted. Then:

  1. Refreshed all pacman keys manually and populated them
  2. Cleared the cache with pacman -Scc
  3. Found packaged being not corrupted anymore
  4. Updated everything successfully with pacman -SYu

The problem is still there.

Update:
7. Updating dbus-broker failed, too (Dbus update, now system "failed to start"):

[manjaro /]# pacman -S dbus-broker
warning: dbus-broker-36-4 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...

Packages (1) dbus-broker-36-4

Total Installed Size:  0.35 MiB
Net Upgrade Size:      0.00 MiB

:: Proceed with installation? [Y/n] Y
(1/1) checking keys in keyring                                     [####################################] 100%
(1/1) checking package integrity                                   [####################################] 100%
(1/1) loading package files                                        [####################################] 100%
(1/1) checking for file conflicts                                  [####################################] 100%
(1/1) checking available disk space                                [####################################] 100%
:: Running pre-transaction hooks...
(1/1) Creating Timeshift snapshot before upgrade...
==> skipping timeshift-autosnap due skipRsyncAutosnap in /etc/timeshift-autosnap.conf set to TRUE.
:: Processing package changes...
(1/1) reinstalling dbus-broker                                     [####################################] 100%
ldconfig: File /usr/lib/libpamac-flatpak.so is empty, not checked.
ldconfig: File /usr/lib/libpamac-flatpak.so.11 is empty, not checked.
ldconfig: File /usr/lib/libpamac.so.11 is empty, not checked.
ldconfig: File /usr/lib/libpamac-gtk.so is empty, not checked.
ldconfig: File /usr/lib/libpamac-aur.so is empty, not checked.
ldconfig: File /usr/lib/libpamac-aur.so.11.7 is empty, not checked.
ldconfig: File /usr/lib/libpamac-appstream.so is empty, not checked.
ldconfig: File /usr/lib/libpamac-aur.so.11 is empty, not checked.
ldconfig: File /usr/lib/libpamac.so is empty, not checked.
ldconfig: File /usr/lib/libpamac.so.11.7 is empty, not checked.
ldconfig: File /usr/lib/libpamac-appstream.so.11 is empty, not checked.
ldconfig: File /usr/lib/libpamac-appstream.so.11.7 is empty, not checked.
ldconfig: File /usr/lib/libpamac-flatpak.so.11.7 is empty, not checked.
:: Running post-transaction hooks...
(1/5) Updating journal message catalog...
(2/5) Reloading system manager configuration...
  Skipped: Running in chroot.
(3/5) Reloading user manager configuration...
  Skipped: Running in chroot.
(4/5) Arming ConditionNeedsUpdate...
(5/5) Refreshing PackageKit...
Error connecting: Could not connect: No such file or directory
error: command failed to execute correctly

Problem is still there.

Can someone please help? What should I post from chroot environment in order to narrow down the problem?

Thanks!#

I initially assumed this was a typo…

Please use:

sudo pacman -Syu

Indeed, it might be beneficial to re-sort the mirrors used before performing the update; something like:

sudo pacman-mirrors --fasttrack && sudo pacman -Syu

Or, substitute --fasttrack for --continent if you prefer.

There was a dbus-broker related issue several months ago, but I doubt that is relevant any longer. What is relevant is that many of the libpamac-* files appear to be corrupted.

You might try using pacman to remove pamac, and install it again while also sorting mirrors.

Some system information will no doubt be helpful to others wishing to help:

inxi --admin --verbosity=8 --filter --no-host --width

sudo pacman -Syu was most likely a typo, thanks!

In fact this was also conducted: pacman-mirrors --fasttrack && sudo pacman -Syu.

Reinstalling pamac leads to error, too:

[manjaro /]# pacman -Syu pamac
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
warning: pamac-gtk-11.7.2-0 is up to date -- reinstalling
:: Starting full system upgrade...
resolving dependencies...
looking for conflicting packages...

Packages (1) pamac-gtk-11.7.2-0

Total Installed Size:  0.53 MiB

:: Proceed with installation? [Y/n] Y
(1/1) checking keys in keyring                                     [####################################] 100%
(1/1) checking package integrity                                   [####################################] 100%
(1/1) loading package files                                        [####################################] 100%
(1/1) checking for file conflicts                                  [####################################] 100%
error: failed to commit transaction (conflicting files)
pamac-gtk: /etc/xdg/autostart/pamac-tray-budgie.desktop exists in filesystem
pamac-gtk: /etc/xdg/autostart/pamac-tray.desktop exists in filesystem
pamac-gtk: /usr/bin/pamac-installer exists in filesystem
pamac-gtk: /usr/bin/pamac-manager exists in filesystem
pamac-gtk: /usr/bin/pamac-tray exists in filesystem
pamac-gtk: /usr/lib/libpamac-gtk.so exists in filesystem
pamac-gtk: /usr/share/applications/org.manjaro.pamac.manager.desktop exists in filesystem
pamac-gtk: /usr/share/applications/pamac-installer.desktop exists in filesystem
pamac-gtk: /usr/share/dbus-1/services/org.manjaro.pamac.manager.service exists in filesystem
pamac-gtk: /usr/share/gnome-shell/extensions/pamac-updates@manjaro.org/README.md exists in filesystem
pamac-gtk: /usr/share/gnome-shell/extensions/pamac-updates@manjaro.org/extension.js exists in filesystem
pamac-gtk: /usr/share/gnome-shell/extensions/pamac-updates@manjaro.org/metadata.json exists in filesystem
pamac-gtk: /usr/share/gnome-shell/extensions/pamac-updates@manjaro.org/stylesheet.css exists in filesystem
pamac-gtk: /usr/share/gnome-shell/search-providers/org.manjaro.pamac.manager.search-provider.ini exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/16x16/apps/system-software-install.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/32x32/apps/system-software-install.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/48x48/apps/system-software-install.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/actions/view-sidebar-end-symbolic.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/actions/view-sidebar-start-symbolic.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/emblems/globe-symbolic.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/installed-check.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/pamac-tray-no-update.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/pamac-tray-update.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/software-install-symbolic.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/software-remove-symbolic.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/software-select-symbolic.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/software-update-symbolic.svg exists in filesystem
Errors occurred, no packages were upgraded.

Command
inxi --admin --verbosity=8 --filter --no-host --width gives no output (within chroot).

I should probably add the information that I chrooted manually, following this excellent guide ([HowTo] Chroot from or into any Linux distribution), instead of using manjaro-chroot -a (since my drives are encrypted).

Actually, I was thinking that you should first uninstall pamac, reboot, and then install it again. This may or may not resolve the issue, but is worth trying to start with.

As the files in question are all related to pamac-gtk, try:

sudo pacman -Rns pamac-gtk

(Reboot for good measure) and then:

sudo pacman -Syu pamac-gtk

With any luck that might solve the pamac-gtk issue.


[quote=“dano, post:1, topic:170643”]
Updating dbus-broker failed
[/quote

I should point out that updating dbus-broker did not fail; you simply did it wrong.

Notice that this is merely a warning that dbus-broker (the same version) is already installed.

If you want to update a package in Manjaro, you only need one command:

sudo pacman -Syu

What you did was to try and install dbus-broker; the same version was already installed. In any case, it’s best to avoid updating single packages as this can potentially leave you in an unsupported state.

Manjaro packages should not be updated individually. Possible exceptions include containerised apps and packages from the AUR.


As I’m largely unfamiliar with luks on Manjaro I’m unable to help with troubleshooting encrypted partitions. From what I’ve managed to glean from your previous posts it’s quite possible you have more corruption; as yet undiscovered.

The fastest way back to a working system may well be to reinstall from scratch. If you opt to do that, I’d suggest not encrypting during install (it can be done later) and make absolutely sure everything works as expected before encrypting.

Yes, you should probably have included that information.

Also, if you are using BTRFS, that would be a vital tidbit to add to the first post, as it drastically changes procedures that might be needed to both diagnose or repair the system.

Some more links that may soon be useful:

Please provide the inxi output from the Manjaro Live Installer environment instead. Some information may not be as accurate, but it should still indicate enough to be useful to others wishing to help.

The community repo hasn’t existed for over a year. This isn’t a major issue in itself, but it is a solid indicator that your system hasn’t been maintained as well as it could have been.

Please see:

And research as much as you can about .pacnew and .pacsave files, and the importance of attending to them.

… a lot of “exists in filesystem” errors
there is very likely more of the same if you go digging

this all sounds to me that you should use your snapshots
and revert to an earlier one - not just the most recent one
and proceed from there

1 Like

@Nachlese, there is no system snapshot!

@soundofthunder, I apologize for the missing information: My HDD is ext4.

This is the system info:

inxi --admin --verbosity=8 --filter --no-host --width                                   ✔ 
System:
  Kernel: 6.10.13-3-MANJARO arch: x86_64 bits: 64 compiler: gcc v: 14.2.1
    clocksource: tsc avail: acpi_pm parameters: BOOT_IMAGE=/boot/vmlinuz-x86_64
    lang=en_US keytable=de tz=UTC misobasedir=manjaro
    misolabel=MANJARO_KDE_2412 quiet systemd.show_status=1 splash driver=free
    nouveau.modeset=1 i915.modeset=1 radeon.modeset=1
  Desktop: KDE Plasma v: 6.1.5 tk: Qt v: N/A info: frameworks v: 6.6.0
    wm: kwin_x11 vt: 2 dm: SDDM Distro: Manjaro base: Arch Linux
Machine:
  Type: Laptop System: HP product: HP EliteBook 830 G6 v: SBKPF
    serial: <superuser required> Chassis: type: 10 serial: <superuser required>
  Mobo: HP model: 854A v: KBC Version 52.6F.00 serial: <superuser required>
    part-nu: 8NW86EC#ABD uuid: <superuser required> UEFI: HP v: R70 Ver. 01.27.00
    date: 12/19/2023
Battery:
  ID-1: BAT0 charge: 24.7 Wh (73.5%) condition: 33.6/50.2 Wh (67.0%)
    volts: 11.5 min: 11.6 model: Hewlett-Packard Primary type: Li-ion
    serial: <filter> status: discharging cycles: 20
Memory:
  System RAM: total: 32 GiB available: 31.04 GiB used: 3.17 GiB (10.2%)
  Message: For most reliable report, use superuser + dmidecode.
  Array-1: capacity: 32 GiB slots: 2 modules: 2 EC: None
    max-module-size: 16 GiB note: est.
  Device-1: Bottom-Slot 1(left) type: DDR4 detail: synchronous size: 16 GiB
    speed: 2400 MT/s volts: curr: 1 width (bits): data: 64 total: 64
    manufacturer: Kingston part-no: 9905744-005.A00G serial: <filter>
  Device-2: Bottom-Slot 2(right) type: DDR4 detail: synchronous size: 16 GiB
    speed: 2400 MT/s volts: curr: 1 width (bits): data: 64 total: 64
    manufacturer: Kingston part-no: 9905744-005.A00G serial: <filter>
PCI Slots:
  Permissions: Unable to run dmidecode. Root privileges required.
CPU:
  Info: model: Intel Core i5-8365U bits: 64 type: MT MCP
    arch: Comet/Whiskey Lake note: check gen: core 8 level: v3 note: check
    built: 2018 process: Intel 14nm family: 6 model-id: 0x8E (142)
    stepping: 0xC (12) microcode: 0xFC
  Topology: cpus: 1x dies: 1 clusters: 4 cores: 4 threads: 8 tpc: 2
    smt: enabled cache: L1: 256 KiB desc: d-4x32 KiB; i-4x32 KiB L2: 1024 KiB
    desc: 4x256 KiB L3: 6 MiB desc: 1x6 MiB
  Speed (MHz): avg: 800 min/max: 400/4100 scaling: driver: intel_pstate
    governor: powersave cores: 1: 800 2: 800 3: 800 4: 800 5: 800 6: 800 7: 800
    8: 800 bogomips: 30409
  Flags: 3dnowprefetch abm acpi adx aes aperfmperf apic arat
    arch_capabilities arch_perfmon art avx avx2 bmi1 bmi2 bts clflush
    clflushopt cmov constant_tsc cpuid cpuid_fault cx16 cx8 de ds_cpl dtes64
    dtherm dts epb ept ept_ad erms est f16c flexpriority flush_l1d fma fpu
    fsgsbase fxsr ht hwp hwp_act_window hwp_epp hwp_notify ibpb ibrs
    ibrs_enhanced ida intel_pt invpcid lahf_lm lm mca mce md_clear mmx monitor
    movbe mpx msr mtrr nonstop_tsc nopl nx pae pat pbe pcid pclmulqdq pdcm
    pdpe1gb pebs pge pln pni popcnt pse pse36 pts rdrand rdseed rdtscp
    rep_good sdbg sep sgx smap smep smx ss ssbd sse sse2 sse4_1 sse4_2 ssse3
    stibp syscall tm tm2 tpr_shadow tsc tsc_adjust tsc_deadline_timer vme vmx
    vnmi vpid x2apic xgetbv1 xsave xsavec xsaveopt xsaves xtopology xtpr
  Vulnerabilities:
  Type: gather_data_sampling mitigation: Microcode
  Type: itlb_multihit status: KVM: VMX disabled
  Type: l1tf status: Not affected
  Type: mds status: Not affected
  Type: meltdown status: Not affected
  Type: mmio_stale_data mitigation: Clear CPU buffers; SMT vulnerable
  Type: reg_file_data_sampling status: Not affected
  Type: retbleed mitigation: Enhanced IBRS
  Type: spec_rstack_overflow status: Not affected
  Type: spec_store_bypass mitigation: Speculative Store Bypass disabled via
    prctl
  Type: spectre_v1 mitigation: usercopy/swapgs barriers and __user pointer
    sanitization
  Type: spectre_v2 mitigation: Enhanced / Automatic IBRS; IBPB: conditional;
    RSB filling; PBRSB-eIBRS: SW sequence; BHI: SW loop, KVM: SW loop
  Type: srbds mitigation: Microcode
  Type: tsx_async_abort mitigation: TSX disabled
Graphics:
  Device-1: Intel WhiskeyLake-U GT2 [UHD Graphics 620] vendor: Hewlett-Packard
    driver: i915 v: kernel arch: Gen-9.5 process: Intel 14nm built: 2016-20
    ports: active: eDP-1 empty: DP-1, DP-2, DP-3, HDMI-A-1, HDMI-A-2, HDMI-A-3
    bus-ID: 00:02.0 chip-ID: 8086:3ea0 class-ID: 0300
  Device-2: Quanta HP HD Camera driver: uvcvideo type: USB rev: 2.0
    speed: 480 Mb/s lanes: 1 mode: 2.0 bus-ID: 1-9:3 chip-ID: 0408:5343
    class-ID: 0e02 serial: <filter>
  Display: x11 server: X.Org v: 21.1.14 with: Xwayland v: 24.1.4
    compositor: kwin_x11 driver: X: loaded: modesetting alternate: fbdev,vesa
    dri: iris gpu: i915 display-ID: :0 screens: 1
  Screen-1: 0 s-res: 1920x1080 s-dpi: 96 s-size: 508x285mm (20.00x11.22")
    s-diag: 582mm (22.93")
  Monitor-1: eDP-1 model: ChiMei InnoLux 0x1392 built: 2018 res: 1920x1080
    hz: 60 dpi: 166 gamma: 1.2 chroma: red: x: 0.592 y: 0.349 green: x: 0.329
    y: 0.557 blue: x: 0.153 y: 0.118 white: x: 0.314 y: 0.329
    size: 293x165mm (11.54x6.5") diag: 336mm (13.2") ratio: 16:9
    modes: 1920x1080
  EDID-Warnings: 1: parse_edid: unknown flag 2
  API: EGL v: 1.5 hw: drv: intel iris platforms: device: 0 drv: iris
    device: 1 drv: swrast gbm: drv: iris surfaceless: drv: iris x11: drv: iris
    inactive: wayland
  API: OpenGL v: 4.6 compat-v: 4.5 vendor: intel mesa v: 24.2.4-arch1.0.1
    glx-v: 1.4 direct-render: yes renderer: Mesa Intel UHD Graphics 620 (WHL GT2)
    device-ID: 8086:3ea0 memory: 15.15 GiB unified: yes
  API: Vulkan v: 1.3.295 layers: N/A device: 0 type: integrated-gpu
    name: Intel UHD Graphics 620 (WHL GT2) driver: mesa intel v: 24.2.4-arch1.0.1
    device-ID: 8086:3ea0 surfaces: xcb,xlib
Audio:
  Device-1: Intel Cannon Point-LP High Definition Audio vendor: Hewlett-Packard
    driver: sof-audio-pci-intel-cnl alternate: snd_hda_intel, snd_soc_skl,
    snd_soc_avs, snd_sof_pci_intel_cnl bus-ID: 00:1f.3 chip-ID: 8086:9dc8
    class-ID: 0401
  API: ALSA v: k6.10.13-3-MANJARO status: kernel-api with: aoss
    type: oss-emulator tools: alsactl,alsamixer,amixer
  Server-1: JACK v: 1.9.22 status: off tools: N/A
  Server-2: PipeWire v: 1.2.5 status: active with: 1: pipewire-pulse
    status: active 2: wireplumber status: active 3: pipewire-alsa type: plugin
    tools: pactl,pw-cat,pw-cli,wpctl
Network:
  Device-1: Intel Cannon Point-LP CNVi [Wireless-AC] driver: iwlwifi v: kernel
    bus-ID: 00:14.3 chip-ID: 8086:9df0 class-ID: 0280
  IF: wlp0s20f3 state: up mac: <filter>
  IP v4: <filter> type: dynamic noprefixroute scope: global
    broadcast: <filter>
  IP v6: <filter> type: dynamic noprefixroute scope: global
  IP v6: <filter> type: dynamic noprefixroute scope: global
  IP v6: <filter> type: noprefixroute scope: link
  Device-2: Intel Ethernet I219-LM vendor: Hewlett-Packard driver: e1000e
    v: kernel port: N/A bus-ID: 00:1f.6 chip-ID: 8086:15bd class-ID: 0200
  IF: enp0s31f6 state: down mac: <filter>
  IF-ID-1: wwan0 state: down mac: N/A
  Info: services: NetworkManager, systemd-timesyncd, wpa_supplicant
  WAN IP: <filter>
Bluetooth:
  Device-1: Intel Bluetooth 9460/9560 Jefferson Peak (JfP) driver: btusb v: 0.8
    type: USB rev: 2.0 speed: 12 Mb/s lanes: 1 mode: 1.1 bus-ID: 1-10:4
    chip-ID: 8087:0aaa class-ID: e001
  Report: rfkill ID: hci0 rfk-id: 0 state: up address: see --recommends
Logical:
  Message: No logical block device data found.
  Device-1: boot_crypt maj-min: 254:0 type: LUKS dm: dm-0 size: 250 GiB
  Components:
  p-1: nvme0n1p2 maj-min: 259:2 size: 250 GiB
RAID:
  Message: No RAID data found.
Drives:
  Local Storage: total: 960.15 GiB used: 150.83 GiB (15.7%)
  SMART Message: Unable to run smartctl. Root privileges required.
  ID-1: /dev/nvme0n1 maj-min: 259:0 vendor: Samsung
    model: SSD 970 EVO Plus 1TB size: 931.51 GiB block-size: physical: 512 B
    logical: 512 B speed: 31.6 Gb/s lanes: 4 tech: SSD serial: <filter>
    fw-rev: 2B2QEXM7 temp: 32.9 C scheme: GPT
  ID-2: /dev/sda maj-min: 8:0 vendor: SanDisk model: Ultra Fit
    size: 28.64 GiB block-size: physical: 512 B logical: 512 B type: USB rev: 3.0
    spd: 5 Gb/s lanes: 1 mode: 3.2 gen-1x1 tech: N/A serial: <filter>
    fw-rev: 1.00 scheme: MBR
  SMART Message: Unknown USB bridge. Flash drive/Unsupported enclosure?
  Message: No optical or floppy data found.
Partition:
  ID-1: /chroot raw-size: 250 GiB size: 245.02 GiB (98.01%)
    used: 150.79 GiB (61.5%) fs: ext4 dev: /dev/dm-0 maj-min: 254:0
    mapped: boot_crypt label: N/A uuid: N/A
  ID-2: /chroot/boot/efi raw-size: 300 MiB size: 299.4 MiB (99.80%)
    used: 43.6 MiB (14.6%) fs: vfat dev: /dev/nvme0n1p1 maj-min: 259:1
    label: NO_LABEL uuid: CD10-10B9
Swap:
  Alert: No swap data was found.
Unmounted:
  ID-1: /dev/sda1 maj-min: 8:1 size: 3.87 GiB fs: iso9660
  ID-2: /dev/sda2 maj-min: 8:2 size: 4 MiB fs: vfat label: MISO_EFI
    uuid: 8BF0-EDB3
USB:
  Hub-1: 1-0:1 info: hi-speed hub with single TT ports: 12 rev: 2.0
    speed: 480 Mb/s (57.2 MiB/s) lanes: 1 mode: 2.0 chip-ID: 1d6b:0002
    class-ID: 0900
  Device-1: 1-8:2 info: Synaptics Fingerprint reader [HP G6]
    type: <vendor specific> driver: N/A interfaces: 1 rev: 2.0
    speed: 12 Mb/s (1.4 MiB/s) lanes: 1 mode: 1.1 power: 100mA
    chip-ID: 06cb:00b7 class-ID: ff00 serial: <filter>
  Device-2: 1-9:3 info: Quanta HP HD Camera type: video driver: uvcvideo
    interfaces: 4 rev: 2.0 speed: 480 Mb/s (57.2 MiB/s) lanes: 1 mode: 2.0
    power: 500mA chip-ID: 0408:5343 class-ID: 0e02 serial: <filter>
  Device-3: 1-10:4 info: Intel Bluetooth 9460/9560 Jefferson Peak (JfP)
    type: bluetooth driver: btusb interfaces: 2 rev: 2.0
    speed: 12 Mb/s (1.4 MiB/s) lanes: 1 mode: 1.1 power: 100mA
    chip-ID: 8087:0aaa class-ID: e001
  Hub-2: 2-0:1 info: super-speed hub ports: 6 rev: 3.1
    speed: 10 Gb/s (1.16 GiB/s) lanes: 1 mode: 3.2 gen-2x1 chip-ID: 1d6b:0003
    class-ID: 0900
  Device-1: 2-2:2 info: SanDisk Ultra Fit type: mass storage
    driver: usb-storage interfaces: 1 rev: 3.0 speed: 5 Gb/s (596.0 MiB/s)
    lanes: 1 mode: 3.2 gen-1x1 power: 896mA chip-ID: 0781:5583 class-ID: 0806
    serial: <filter>
  Hub-3: 3-0:1 info: hi-speed hub with single TT ports: 2 rev: 2.0
    speed: 480 Mb/s (57.2 MiB/s) lanes: 1 mode: 2.0 chip-ID: 1d6b:0002
    class-ID: 0900
  Hub-4: 4-0:1 info: super-speed hub ports: 2 rev: 3.1
    speed: 10 Gb/s (1.16 GiB/s) lanes: 1 mode: 3.2 gen-2x1 chip-ID: 1d6b:0003
    class-ID: 0900
Sensors:
  System Temperatures: cpu: 38.0 C pch: 34.0 C mobo: N/A
  Fan Speeds (rpm): N/A
Repos:
  Packages: pm: pacman pkgs: 1267 libs: 331 tools: pamac pm: flatpak pkgs: 0
  Active pacman repo servers in: /etc/pacman.d/mirrorlist
    1: https://mirror1.sox.rs/manjaro/stable/$repo/$arch
    2: https://mirrors.sonic.net/manjaro/stable/$repo/$arch
    3: https://mirror.nyist.edu.cn/manjaro/stable/$repo/$arch
    4: https://ftp.gwdg.de/pub/linux/manjaro/stable/$repo/$arch
    5: http://mirror.datacenter.by/pub/mirrors/manjaro/stable/$repo/$arch
    6: https://mirrors.sjtug.sjtu.edu.cn/manjaro/stable/$repo/$arch
    7: https://opencolo.mm.fcix.net/manjaro/stable/$repo/$arch
    8: https://ftp.linux.org.tr/manjaro/stable/$repo/$arch
    9: https://mirrors.xtom.ee/manjaro/stable/$repo/$arch
    10: https://mirror.kamtv.ru/manjaro/stable/$repo/$arch
    11: https://mirror.koddos.net/manjaro/stable/$repo/$arch
    12: http://ftp.uni-kl.de/pub/linux/manjaro/stable/$repo/$arch
    13: https://ask4.mm.fcix.net/manjaro/stable/$repo/$arch
    14: http://mirror.terrahost.no/linux/manjaro/stable/$repo/$arch
    15: https://mirror.bouwhuis.network/manjaro/stable/$repo/$arch
    16: https://mirror.truenetwork.ru/manjaro/stable/$repo/$arch
    17: https://mirror.alpix.eu/manjaro/stable/$repo/$arch
    18: https://repo.iut.ac.ir/repo/manjaro/stable/$repo/$arch
    19: https://mirrors.aliyun.com/manjaro/stable/$repo/$arch
    20: https://mirror.easyname.at/manjaro/stable/$repo/$arch
    21: https://cofractal-ewr.mm.fcix.net/manjaro/stable/$repo/$arch
    22: https://ftp.nluug.nl/pub/os/Linux/distr/manjaro/stable/$repo/$arch
    23: http://ftp.dei.uc.pt/pub/linux/manjaro/stable/$repo/$arch
    24: https://codingflyboy.mm.fcix.net/manjaro/stable/$repo/$arch
    25: https://uvermont.mm.fcix.net/manjaro/stable/$repo/$arch
    26: https://mirror.yandex.ru/mirrors/manjaro/stable/$repo/$arch
    27: https://mirror.albony.xyz/manjaro/stable/$repo/$arch
    28: https://mirror.ibakerserver.pt/manjaro/stable/$repo/$arch
    29: https://coresite.mm.fcix.net/manjaro/stable/$repo/$arch
    30: https://repo.ialab.dsu.edu/manjaro/stable/$repo/$arch
    31: https://mirror.telepoint.bg/manjaro/stable/$repo/$arch
    32: https://mirror.csclub.uwaterloo.ca/manjaro/stable/$repo/$arch
    33: https://mirror.freedif.org/Manjaro/stable/$repo/$arch
    34: http://manjaro.grena.ge/stable/$repo/$arch
    35: https://mirrors2.manjaro.org/stable/$repo/$arch
    36: https://mirrors.tuna.tsinghua.edu.cn/manjaro/stable/$repo/$arch
    37: https://mirror.it4i.cz/manjaro/stable/$repo/$arch
    38: https://mirror.math.princeton.edu/pub/manjaro/stable/$repo/$arch
    39: https://ftp.lysator.liu.se/pub/manjaro/stable/$repo/$arch
    40: http://ftp.tu-chemnitz.de/pub/linux/manjaro/stable/$repo/$arch
    41: https://mirrors.dotsrc.org/manjaro/stable/$repo/$arch
    42: https://mirror.aarnet.edu.au/pub/manjaro/stable/$repo/$arch
    43: https://manjaro.mirror.liquidtelecom.com/stable/$repo/$arch
    44: http://ftp.rz.tu-bs.de/pub/mirror/manjaro.org/repos/stable/$repo/$arch
    45: https://ftp.caliu.cat/pub/distribucions/manjaro/stable/$repo/$arch
    46: http://ftp.belnet.be/mirrors/manjaro/repos/stable/$repo/$arch
    47: https://manjaro.mirror.garr.it/manjaro/stable/$repo/$arch
    48: http://manjaro.mirror.ac.za/stable/$repo/$arch
    49: https://nocix.mm.fcix.net/manjaro/stable/$repo/$arch
    50: http://ftp.snt.utwente.nl/pub/linux/manjaro/stable/$repo/$arch
    51: https://ftp.cc.uoc.gr/mirrors/linux/manjaro/stable/$repo/$arch
    52: https://repos.silknet.com/manjaro/stable/$repo/$arch
    53: https://manjaro.repo.cure.edu.uy/stable/$repo/$arch
    54: https://mirrors.ustc.edu.cn/manjaro/stable/$repo/$arch
    55: https://linorg.usp.br/manjaro/stable/$repo/$arch
    56: http://mirror.xeonbd.com/manjaro/stable/$repo/$arch
    57: https://mirrors.ocf.berkeley.edu/manjaro/stable/$repo/$arch
    58: https://muug.ca/mirror/manjaro/stable/$repo/$arch
    59: https://edgeuno-bog2.mm.fcix.net/manjaro/stable/$repo/$arch
    60: https://mirror.archlinux.tw/Manjaro/stable/$repo/$arch
    61: https://mirror.init7.net/manjaro/stable/$repo/$arch
    62: http://ftp.riken.jp/Linux/manjaro/stable/$repo/$arch
    63: https://mirror.funami.tech/manjaro/stable/$repo/$arch
    64: https://mirrors.piconets.webwerks.in/manjaro-mirror/stable/$repo/$arch
    65: http://ftp.tsukuba.wide.ad.jp/Linux/manjaro/stable/$repo/$arch
    66: https://mirrors.jlu.edu.cn/manjaro/stable/$repo/$arch
    67: https://mirrors.gigenet.com/manjaro/stable/$repo/$arch
    68: http://mirror.is.co.za/mirrors/manjaro.org/stable/$repo/$arch
    69: https://mirror.bardia.tech/manjaro/stable/$repo/$arch
    70: http://ossmirror.mycloud.services/os/linux/manjaro/stable/$repo/$arch
    71: https://bd.mirror.vanehost.com/Manjaro/stable/$repo/$arch
    72: http://manjaro.mirrors.theom.nz/manjaro/stable/$repo/$arch
    73: https://manjaro.ipacct.com/manjaro/stable/$repo/$arch
    74: https://www.mirrorservice.org/sites/repo.manjaro.org/repos/stable/$repo/$arch
    75: http://manjaro.mirrors.uk2.net/stable/$repo/$arch
    76: https://manjaro.mirrors.lavatech.top/stable/$repo/$arch
    77: https://manjaro.kurdy.org/stable/$repo/$arch
    78: https://mirrors.pku.edu.cn/manjaro/stable/$repo/$arch
    79: https://mirror.ufro.cl/manjaro/stable/$repo/$arch
    80: https://quantum-mirror.hu/mirrors/pub/manjaro/stable/$repo/$arch
    81: https://ftpmirror1.infania.net/mirror/manjaro/stable/$repo/$arch
    82: https://mirror.seahost.de/manjaro/stable/$repo/$arch
    83: https://mirror.vinehost.net/manjaro/stable/$repo/$arch
    84: https://mnvoip.mm.fcix.net/manjaro/stable/$repo/$arch
    85: http://mirror.fcix.net/manjaro/stable/$repo/$arch
    86: https://mirror.futureweb.be/manjaro/stable/$repo/$arch
    87: https://mirror.nju.edu.cn/manjaro/stable/$repo/$arch
    88: https://mirror.ufam.edu.br/manjaro/stable/$repo/$arch
    89: https://mirrors.ft.uam.es/manjaro/stable/$repo/$arch
    90: https://mirrors.netix.net/manjaro/stable/$repo/$arch
    91: https://manjaro.mirror.wearetriple.com/stable/$repo/$arch
    92: https://manjarolinux-mirror.cloud.mu/stable/$repo/$arch
    93: https://mirrors.xtom.de/manjaro/stable/$repo/$arch
    94: https://mirrors.xtom.jp/manjaro/stable/$repo/$arch
    95: https://ct.mirror.garr.it/mirrors/manjaro/stable/$repo/$arch
    96: https://mirror.zetup.net/manjaro/stable/$repo/$arch
    97: https://ba.mirror.garr.it/mirrors/manjaro/stable/$repo/$arch
    98: https://fosszone.csd.auth.gr/manjaro/stable/$repo/$arch
    99: https://forksystems.mm.fcix.net/manjaro/stable/$repo/$arch
    100: https://mirror.dkm.cz/manjaro/stable/$repo/$arch
    101: https://mirrors.atlas.net.co/manjaro/stable/$repo/$arch
    102: https://ftp.psnc.pl/linux/manjaro/stable/$repo/$arch
    103: https://volico.mm.fcix.net/manjaro/stable/$repo/$arch
    104: https://mirrors.nic.cz/manjaro/stable/$repo/$arch
    105: https://manjaro.ynh.ovh/stable/$repo/$arch
    106: https://mirror.dc.uz/manjaro/stable/$repo/$arch
    107: http://ftp.free.org/mirrors/repo.manjaro.org/repos/stable/$repo/$arch
    108: https://mirror.23m.com/manjaro/stable/$repo/$arch
    109: https://mirror.kku.ac.th/manjaro/stable/$repo/$arch
    110: https://mirrors.up.pt/pub/manjaro/stable/$repo/$arch
    111: https://ftp.halifax.rwth-aachen.de/manjaro/stable/$repo/$arch
    112: https://mirror.phoepsilonix.love/manjaro/stable/$repo/$arch
    113: https://mirror.xenyth.net/manjaro/stable/$repo/$arch
    114: https://mirrors.ucr.ac.cr/manjaro/stable/$repo/$arch
    115: https://manjaro.c3sl.ufpr.br/stable/$repo/$arch
    116: https://ipng.mm.fcix.net/manjaro/stable/$repo/$arch
    117: https://mirrors.cicku.me/manjaro/stable/$repo/$arch
    118: https://mirror.2degrees.nz/manjaro/stable/$repo/$arch
    119: https://ziply.mm.fcix.net/manjaro/stable/$repo/$arch
    120: https://ridgewireless.mm.fcix.net/manjaro/stable/$repo/$arch
    121: http://kartolo.sby.datautama.net.id/manjaro/stable/$repo/$arch
    122: https://southfront.mm.fcix.net/manjaro/stable/$repo/$arch
    123: https://irltoolkit.mm.fcix.net/manjaro/stable/$repo/$arch
    124: https://mirror.netcologne.de/manjaro/stable/$repo/$arch
    125: https://fastmirror.pp.ua/manjaro/stable/$repo/$arch
    126: https://ohioix.mm.fcix.net/manjaro/stable/$repo/$arch
    127: https://gsl-syd.mm.fcix.net/manjaro/stable/$repo/$arch
    128: https://nnenix.mm.fcix.net/manjaro/stable/$repo/$arch
    129: http://free.nchc.org.tw/manjaro/stable/$repo/$arch
    130: https://mirror.alwyzon.net/manjaro/stable/$repo/$arch
    131: https://mirrors.manjaro.org/repo/stable/$repo/$arch
Processes:
  CPU top: 5 of 248
  1: cpu: 100% command: ps pid: 34985 mem: 3.40 MiB (0.0%)
  2: cpu: 13.1% command: firefox pid: 2180 mem: 476.6 MiB (1.4%)
  3: cpu: 7.5% command: zsh pid: 34829 mem: 8.22 MiB (0.0%)
  4: cpu: 4.3% command: firefox pid: 2475 mem: 258.4 MiB (0.8%)
  5: cpu: 2.9% command: kwin_x11 pid: 1252 mem: 187.9 MiB (0.5%)
  Memory top: 5 of 248
  1: mem: 476.6 MiB (1.4%) command: firefox pid: 2180 cpu: 13.1%
  2: mem: 351.2 MiB (1.1%) command: plasmashell pid: 1295 cpu: 0.7%
  3: mem: 258.4 MiB (0.8%) command: firefox pid: 2475 cpu: 4.3%
  4: mem: 231.7 MiB (0.7%) command: konsole pid: 2763 cpu: 0.4%
  5: mem: 201.7 MiB (0.6%) command: firefox pid: 2599 cpu: 1.0%
Info:
  Processes: 248 Power: uptime: 43m states: freeze,mem,disk suspend: deep
    avail: s2idle wakeups: 0 hibernate: platform avail: shutdown, reboot,
    suspend, test_resume image: 12.37 GiB services: org_kde_powerdevil,
    power-profiles-daemon, upowerd Init: systemd v: 256 default: graphical
    tool: systemctl
  Compilers: N/A Shell: Zsh v: 5.9 default: Bash v: 5.2.37
    running-in: konsole inxi: 3.3.36

Uninstalling pamac-gtk worked:

sudo pacman -Rns pamac-gtk

Re-installing, however, failed:

[manjaro /]# pacman -Syu pamac
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
:: There are 2 providers available for pamac:
:: Repository extra
   1) pamac-gtk  2) pamac-gtk3

Enter a number (default=1): 1
:: Starting full system upgrade...
resolving dependencies...
looking for conflicting packages...

Packages (4) archlinux-appstream-data-20240914-1  gtk4-1:4.14.5-1  libadwaita-1:1.5.4-1
             pamac-gtk-11.7.2-0

Total Installed Size:  73.92 MiB

:: Proceed with installation? [Y/n] Y
(4/4) checking keys in keyring                                [##################################] 100%
(4/4) checking package integrity                              [##################################] 100%
(4/4) loading package files                                   [##################################] 100%
(4/4) checking for file conflicts                             [##################################] 100%
error: failed to commit transaction (conflicting files)
pamac-gtk: /etc/xdg/autostart/pamac-tray-budgie.desktop exists in filesystem
pamac-gtk: /etc/xdg/autostart/pamac-tray.desktop exists in filesystem
pamac-gtk: /usr/bin/pamac-installer exists in filesystem
pamac-gtk: /usr/bin/pamac-manager exists in filesystem
pamac-gtk: /usr/bin/pamac-tray exists in filesystem
pamac-gtk: /usr/lib/libpamac-gtk.so exists in filesystem
pamac-gtk: /usr/share/applications/org.manjaro.pamac.manager.desktop exists in filesystem
pamac-gtk: /usr/share/applications/pamac-installer.desktop exists in filesystem
pamac-gtk: /usr/share/dbus-1/services/org.manjaro.pamac.manager.service exists in filesystem
pamac-gtk: /usr/share/gnome-shell/extensions/pamac-updates@manjaro.org/README.md exists in filesystem
pamac-gtk: /usr/share/gnome-shell/extensions/pamac-updates@manjaro.org/extension.js exists in filesystem
pamac-gtk: /usr/share/gnome-shell/extensions/pamac-updates@manjaro.org/metadata.json exists in filesystem
pamac-gtk: /usr/share/gnome-shell/extensions/pamac-updates@manjaro.org/stylesheet.css exists in filesystem
pamac-gtk: /usr/share/gnome-shell/search-providers/org.manjaro.pamac.manager.search-provider.ini exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/16x16/apps/system-software-install.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/32x32/apps/system-software-install.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/48x48/apps/system-software-install.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/actions/view-sidebar-end-symbolic.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/actions/view-sidebar-start-symbolic.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/emblems/globe-symbolic.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/installed-check.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/pamac-tray-no-update.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/pamac-tray-update.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/software-install-symbolic.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/software-remove-symbolic.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/software-select-symbolic.svg exists in filesystem
pamac-gtk: /usr/share/icons/hicolor/scalable/status/software-update-symbolic.svg exists in filesystem
Errors occurred, no packages were upgraded.

Checking these pacnew and pacsave files yields this:

[manjaro /]# DIFFPROG=meld pacdiff -s
==> pacnew file found for /usr/share/icons/default/index.theme
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] s 
==> pacnew file found for /etc/passwd
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] s
==> pacnew file found for /etc/shells
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] s
==> pacnew file found for /etc/locale.gen
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] s
==> pacnew file found for /etc/default/grub
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] s
==> pacnew file found for /etc/pam.d/kde
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] s
==> pacnew file found for /etc/mkinitcpio.conf
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] s
==> pacnew file found for /etc/pacman.conf
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] s
==> pacnew file found for /etc/makepkg.conf.d/rust.conf
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] s
==> pacnew file found for /etc/pacman-mirrors.conf
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] s
==> pacnew file found for /etc/pam.d/sddm
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] s
==> pacnew file found for /etc/sudoers
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] s
==> pacsave file found for /etc/texmf/web2c/fmtutil.cnf
:: (V)iew, (M)erge, (S)kip, (R)emove pacsave, (O)verwrite with pacsave, (Q)uit: [v/m/s/r/o/q] s
[manjaro /]# 

This somehow looks less severe than from your explanation, but maybe I am comletely wrong, since I still have no clue.

What else should I try?

That’s because you used the wrong command.

You just uninstalled pamac-gtk so even if you had typed the right command, you cannot update a package that no longer installed.

Here is where you should have used:

sudo pacman -S pamac-gtk

to install it again.

Remember, you uninstalled pamac-gtk, not pamac.

Not really.
Well, it is the ‘wrong command’ … but it eventually leads to same transaction and the same errors.

Note the pamac-gtk preface.


You skipped all of them.

Instead they need to be managed.

Use v to view … and then use the opened meld window to compare and merge as needed.
One known example would be the removal of the [community] repo that will be shown in the pacman.conf.pacnew.

Also be aware that meld provides helpful arrow buttons to easily merge things, and to save the file on or before exit.

After properly merged and closed you will be returned to the pacdiff prompt where you can then remove the pacnew file. Or you can skip it again to keep it saved.

Note: Be extra careful about the sudoers one, and maybe even continue to skip it for now.

Managing your pacnews is not optional!

Here is an extra link if needed:


On to your larger issue. In order to try to find all the ‘exists on filesystem’ errors I may suggest targeting all (native) packages for reinstall.

sudo pacman -Syu $(pacman -Qnq)

We may expect more errors in this transaction, but what they are exactly will be informative.

1 Like

whatever gave me the idea that there where …

but:
what do I know what really happened … :man_shrugging:

@cscs , I’ll try to clean-up my packnews, but encounter new problems, most likely related to chroot…

Calling DIFFPROG=meld pacdiff -s and selecting view yields

[manjaro /]# DIFFPROG=meld pacdiff -s
==> pacnew file found for /usr/share/icons/default/index.theme
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] v
sudoedit: unable to find terminal name for device 136, 3
sudoedit: unable to allocate pty: No such device
sudo: unable to find terminal name for device 136, 3
sudo: unable to allocate pty: No such device

I assume this is related to missing pseudo devices from my live environment.

I tried to fix this with additional binding:

mount --bind /dev/pts /chroot/dev/pts

This yields different result:

==> pacnew file found for /usr/share/icons/default/index.theme
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q] v
Authorization required, but no authorization protocol specified

Authorization required, but no authorization protocol specified

Traceback (most recent call last):
  File "/usr/bin/meld", line 462, in <module>
    sys.exit(main())
             ^^^^^^
  File "/usr/bin/meld", line 457, in main
    setup_settings()
  File "/usr/bin/meld", line 316, in setup_settings
    meld.settings.create_settings()
  File "/usr/lib/python3.12/site-packages/meld/settings.py", line 121, in create_settings
    _meldsettings = MeldSettings()
                    ^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/site-packages/meld/settings.py", line 39, in __init__
    self.on_setting_changed(settings, 'prefer-dark-theme')
  File "/usr/lib/python3.12/site-packages/meld/settings.py", line 56, in on_setting_changed
    self.style_scheme = self._style_scheme_from_gsettings()
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/site-packages/meld/settings.py", line 64, in _style_scheme_from_gsettings
    set_base_style_scheme(scheme, prefer_dark)
  File "/usr/lib/python3.12/site-packages/meld/style.py", line 44, in set_base_style_scheme
    gtk_settings.props.gtk_application_prefer_dark_theme = prefer_dark
    ^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'props'
sudoedit: /usr/share/icons/default/index.theme.pacnew unchanged
sudoedit: /usr/share/icons/default/index.theme unchanged

I am a little bit puzzled now, if I am still on the right track. Can you confirm that I need to solve the autorization problem next?

for me, that is not a .pacnew, but a .pacsave

and it is one of the least important of them all as well

diff gives:

diff /usr/share/icons/default/index.theme /usr/share/icons/default/index.theme.pacsave 
1,2c1,2
< [Icon Theme]
< Inherits=Adwaita
---
> [icon theme]
> Inherits=xcursor-breeze

one can make it appear more difficult than it actually is …

the question remains:
why would pacdiff find .pacsave files as well as .pacnew … ?

answer from man pacdiff:

NAME
       pacdiff - pacorig, pacnew and pacsave maintenance utility

so, yeah - it will find both

just use overwrite:
sudo pacman -S pamac-gtk --overwrite "*"
but you may have more corrupted packages…
check also with:
sudo ldconfig
this should return nothing…

1 Like

Ok, I found my mistake: This description helps in order to call GUI app from chroot.

I then continued with cleaning up my pacnews.

Now I am here again, with different picture:

sudo pacman -Syu $(pacman -Qnq)

gives diff

(1495/1495) checking keys in keyring                          [##################################] 100%
(1495/1495) checking package integrity                        [##################################] 100%
(1495/1495) loading package files                             [##################################] 100%
(1495/1495) checking for file conflicts                       [##################################] 100%
error: failed to commit transaction (conflicting files)
inxi: /etc/inxi.conf exists in filesystem
inxi: /usr/bin/inxi exists in filesystem
inxi: /usr/share/man/man1/inxi.1.gz exists in filesystem
xorg-server-common: /usr/lib/xorg/protocol.txt exists in filesystem
xorg-server-common: /usr/share/licenses/xorg-server-common/COPYING exists in filesystem
xorg-server-common: /usr/share/man/man1/Xserver.1.gz exists in filesystem
xorg-server-common: /var/lib/xkb/README.compiled exists in filesystem
xorg-xwayland: /usr/bin/Xwayland exists in filesystem
xorg-xwayland: /usr/lib/pkgconfig/xwayland.pc exists in filesystem
xorg-xwayland: /usr/share/applications/org.freedesktop.Xwayland.desktop exists in filesystem
xorg-xwayland: /usr/share/licenses/xorg-xwayland/COPYING exists in filesystem
xorg-xwayland: /usr/share/man/man1/Xwayland.1.gz exists in filesystem
libpamac: /etc/dbus-1/system.d/org.manjaro.pamac.daemon.conf exists in filesystem
libpamac: /usr/bin/dependency-checker exists in filesystem
libpamac: /usr/bin/outdated-checker exists in filesystem
libpamac: /usr/bin/pamac-checkupdates exists in filesystem
libpamac: /usr/bin/pamac-daemon exists in filesystem
libpamac: /usr/include/pamac.h exists in filesystem
libpamac: /usr/lib/girepository-1.0/Pamac-11.typelib exists in filesystem
libpamac: /usr/lib/libpamac-appstream.so exists in filesystem
libpamac: /usr/lib/libpamac-appstream.so.11 exists in filesystem
libpamac: /usr/lib/libpamac-appstream.so.11.7 exists in filesystem
libpamac: /usr/lib/libpamac-aur.so exists in filesystem
libpamac: /usr/lib/libpamac-aur.so.11 exists in filesystem
libpamac: /usr/lib/libpamac-aur.so.11.7 exists in filesystem
libpamac: /usr/lib/libpamac.so exists in filesystem
libpamac: /usr/lib/libpamac.so.11 exists in filesystem
libpamac: /usr/lib/libpamac.so.11.7 exists in filesystem
libpamac: /usr/lib/pkgconfig/pamac.pc exists in filesystem
libpamac: /usr/lib/systemd/system/pamac-cleancache.service exists in filesystem
libpamac: /usr/lib/systemd/system/pamac-cleancache.timer exists in filesystem
libpamac: /usr/lib/systemd/system/pamac-daemon.service exists in filesystem
libpamac: /usr/lib/systemd/system/pamac-mirrorlist.service exists in filesystem
libpamac: /usr/lib/systemd/system/pamac-mirrorlist.timer exists in filesystem
libpamac: /usr/share/dbus-1/system-services/org.manjaro.pamac.daemon.service exists in filesystem
libpamac: /usr/share/gir-1.0/Pamac-11.gir exists in filesystem
libpamac: /usr/share/locale/af/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ar/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ast/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/az/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/az_AZ/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/be/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/bg/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/bn/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/bs/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ca/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ca@valencia/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/co/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/cs/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/cy/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/da/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/de/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/de_AT/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/de_CH/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/de_DE/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/el/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/el_GR/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/en_GB/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/en_ee/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/eo/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/es/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/es_419/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/es_AR/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/es_ES/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/es_MX/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/es_SV/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/et/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/eu/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/fa/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/fa_IR/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/fi/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/fo/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/fr/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/gl/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/gl_ES/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/gug_PY/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/he/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/he_IL/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/hi/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/hi_IN/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/hr/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/hr_HR/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/hu/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/id/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ie/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/is/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/is_IS/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/it/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/it_IT/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ja/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ka/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/kab/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/kk/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ko/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/lt/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ml/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ms/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/nb/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ne/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ne_NP/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/nl/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/nl_BE/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/nl_NL/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/nn/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/or/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/pl/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/pl_PL/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/pt/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/pt_BR/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/pt_PT/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ro/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ru/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/si/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/sk/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/sl/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/sl_SI/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/sq/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/sq_AL/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/sr/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/sr@latin/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/sr_RS/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/sr_RS@latin/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/sv/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/sw/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ta/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/tr/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/uk/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/ur_PK/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/uz/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/vi/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/zh/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/zh_CN/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/locale/zh_TW/LC_MESSAGES/pamac.mo exists in filesystem
libpamac: /usr/share/mime/packages/x-alpm-package.xml exists in filesystem
libpamac: /usr/share/polkit-1/actions/org.manjaro.pamac.policy exists in filesystem
libpamac: /usr/share/vala/vapi/pamac.vapi exists in filesystem
libpamac-flatpak-plugin: /usr/lib/libpamac-flatpak.so exists in filesystem
libpamac-flatpak-plugin: /usr/lib/libpamac-flatpak.so.11 exists in filesystem
libpamac-flatpak-plugin: /usr/lib/libpamac-flatpak.so.11.7 exists in filesystem
manjaro-release: /etc/lsb-release exists in filesystem
xorg-server: /usr/bin/X exists in filesystem
xorg-server: /usr/bin/Xorg exists in filesystem
xorg-server: /usr/bin/gtf exists in filesystem
xorg-server: /usr/lib/Xorg exists in filesystem
xorg-server: /usr/lib/Xorg.wrap exists in filesystem
xorg-server: /usr/lib/xorg/modules/drivers/modesetting_drv.so exists in filesystem
xorg-server: /usr/lib/xorg/modules/extensions/libglx.so exists in filesystem
xorg-server: /usr/lib/xorg/modules/input/inputtest_drv.so exists in filesystem
xorg-server: /usr/lib/xorg/modules/libexa.so exists in filesystem
xorg-server: /usr/lib/xorg/modules/libfbdevhw.so exists in filesystem
xorg-server: /usr/lib/xorg/modules/libglamoregl.so exists in filesystem
xorg-server: /usr/lib/xorg/modules/libint10.so exists in filesystem
xorg-server: /usr/lib/xorg/modules/libshadow.so exists in filesystem
xorg-server: /usr/lib/xorg/modules/libshadowfb.so exists in filesystem
xorg-server: /usr/lib/xorg/modules/libvgahw.so exists in filesystem
xorg-server: /usr/lib/xorg/modules/libwfb.so exists in filesystem
xorg-server: /usr/share/X11/xorg.conf.d/10-quirks.conf exists in filesystem
xorg-server: /usr/share/licenses/xorg-server/COPYING exists in filesystem
xorg-server: /usr/share/man/man1/Xorg.1.gz exists in filesystem
xorg-server: /usr/share/man/man1/Xorg.wrap.1.gz exists in filesystem
xorg-server: /usr/share/man/man1/gtf.1.gz exists in filesystem
xorg-server: /usr/share/man/man4/exa.4.gz exists in filesystem
xorg-server: /usr/share/man/man4/fbdevhw.4.gz exists in filesystem
xorg-server: /usr/share/man/man4/inputtestdrv.4.gz exists in filesystem
xorg-server: /usr/share/man/man4/modesetting.4.gz exists in filesystem
xorg-server: /usr/share/man/man5/Xwrapper.config.5.gz exists in filesystem
xorg-server: /usr/share/man/man5/xorg.conf.5.gz exists in filesystem
xorg-server: /usr/share/man/man5/xorg.conf.d.5.gz exists in filesystem
Errors occurred, no packages were upgraded.

Then I re-installed these reported packages with pacman -S --overwrite "*" <pck>, since the repos are correct after pacnew cleanup. This may also relate to my initial key issue.

However…

Then I re-installed everything successfully with

sudo pacman -Syu $(pacman -Qnq)

Then I rebooted and now I can successfully open the slot of my luks partition, but the encrpted devices don’t get opened since they cannot be found in /dev/mapper/. I stuck in the rescue shell.

I triple-checked the disk’s uuid and /etc/crypttab (and they should of course not change in my case).

What am I missing now?

does sudo ldconfig outputs anything?
you can provide logs from the failed boot:
journalctl -b-1 -p5 --no-pager

ldconfig

yields nothing.

gives information from my original problem, when there was D-Bus issue reported. It is not related the problem now.

I tried to look at these grub settings (which were also part of my pacnews revision and found something smelly:

menuentry 'Manjaro Linux (Kernel: 6.1.112-1-MANJARO x64)' --class manjaro --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-6.1.112-1-MANJARO x64-advanced-3e5ef021-8d09-4d2e-9ccd-f2c254952e5c' {
        savedefault
                load_video
                set gfxpayload=keep
                insmod gzio
                insmod part_gpt
                insmod cryptodisk
                insmod luks
                insmod gcry_rijndael
                insmod gcry_rijndael
                insmod gcry_sha256
                insmod ext2
                cryptomount -u 794e3e8d-403e-4dcf-9547-3a021ef2f604
                set root='cryptouuid/794e3e8d403e4dcf95473a021ef2f604'
                if [ x$feature_platform_search_hint = xy ]; then
                  search --no-floppy --fs-uuid --set=root --hint='cryptouuid/794e3e8d403e4dcf95473a021ef2f604'  3e5ef021-8d09-4d2e-9ccd-f2c254952e5c
                else
                  search --no-floppy --fs-uuid --set=root 3e5ef021-8d09-4d2e-9ccd-f2c254952e5c
                fi
                linux   /boot/vmlinuz-6.1-x86_64 root=UUID=3e5ef021-8d09-4d2e-9ccd-f2c254952e5c rw  quiet cryptdevice=UUID=794e3e8d-403e-4dcf-9547-3a021ef2f604:luks-794e3e8d-403e-4dcf-9547-3a021ef2f604 root=/dev/mapper/luks-794e3e8d-403e-4dcf-9547-3a021ef2f604 udev.log_priority=3
                initrd  /boot/intel-ucode.img /boot/initramfs-6.1-x86_64.img
        }

In particular, I am confused by this line:

search --no-floppy --fs-uuid --set=root --hint='cryptouuid/794e3e8d403e4dcf95473a021ef2f604'  3e5ef021-8d09-4d2e-9ccd-f2c254952e5c

It would search for the UUID of my thumb drive (from the live system) and report that the boot partition (with different UUID) was not found.

Uuuuuh.

dont use luks/full encryption, so really cant help with that…
can you normally chroot into the encrypted partition?
try booting with a different kernel…

You can open the crypted volume with cryptsetup -v luksOpen /dev/<dev> <mapper_name>. This is the unencrypted boot partition under /dev/mapper/<mapper_name> which can be normally mounted into the chroot environment.

Unfortunately, the UUID from my live system thumb drive will be referenced for all available kernels. This won’t help…

This doesn’t make sense to me.

Boot from live usb.
Do nothing else.

open terminal and issue:
lsblk -f

then, from that, tell what is encrypted and what is not.

open the encrypted container - you know how to do that

… what is inside it?

lsblk -f
once again

This was my bad. I am sorry!!

The UUID is actually related to the open crypt volume…

├─sda1         iso9660     Joliet Extension MANJARO_KDE_2412 2024-11-04-04-24-27-00                              
└─sda2         vfat        FAT12            MISO_EFI         8BF0-EDB3                                           
nvme0n1                                                                                                          
├─nvme0n1p1    vfat        FAT32            NO_LABEL         CD10-10B9                             255.8M    15% /chroot/boot/efi
├─nvme0n1p2    crypto_LUKS 1                                 794e3e8d-403e-4dcf-9547-3a021ef2f604                
│ └─boot_crypt ext4        1.0              System           3e5ef021-8d09-4d2e-9ccd-f2c254952e5c   81.5G    62% /chroot
├─nvme0n1p3    crypto_LUKS 1                                 7f38ff02-ee3b-42f0-8f2d-ebb9ba67de56                
└─nvme0n1p4    crypto_LUKS 1                                 919c4578-3819-48c3-b125-ed4e33881fe7                

It’s the UUID 3e5ef....

I apologize again for the confusion. I should learn grub rescue then and check where it stopped from the shell.

:flushed:

I struggle to see the problem.
everything is encrypted separately
your /boot is now decrypted - and you can mount it somewhere and look at it’s contents

ls -al /dev/mapper/

How did you open/unlock it? What command was used?

One of the other, also encrypted, partitions contain your system root -
with all the information in /etc/fstab and /etc/crypttab.



How did you even chroot with this setup?

It is not difficult, but simply:
manjaro-chroot -a
will not cut it in this case.

You’d have to open all your important encrypted volumes
and mount them in the right order to … somewhere - let’s say: to /mnt

then you’d have to do this:
manjaro-chroot /mnt /bin/bash