[Solved] Power loss when upgrading kernel, unable to install packages

pag-r · 2024-11-10 13:14:07

During a system update (pacman -Syu), during mkintcpio I get power loss. Now system is broken. While trying to reinstall anything I get

ldconfig:File /path/to/file(s) is empty, not checked

. If trying to reinstall linux it fails with error:

Error connecting: Could not connect: Connection refused

. I'm wondering should I run pacman with overwrite option https://wiki.archlinux.org/title/System … n_commands, even though is should be avoided. I'm out of ideas. I already tried bootable arch-chroot approach but this returns

file xyz exists in the system

Last edited by pag-r (2024-11-10 17:43:54)

seth · 2024-11-10 14:36:03

I'm wondering should I run pacman with overwrite option

No.

https://wiki.archlinux.org/title/Pacman … ed_upgrade
You might have to use the pacman from the install iso, make sure it's not tooold™ or you get signature validation issues.

Check what's broken

pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg -Qkk | grep -v ', 0 altered files' | grep -v backup

Every package that shows up there with suspicious file deviations (some, esp. of config files are normal) needs to be re-installed.
Every package that shows up w/ broken or missing mtree needs to be installed --dbonly first, then proper

pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg --dbonly -Sy packages with broken mtrees
pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg -Sy all broken packages including the above ones

pag-r · 2024-11-10 16:17:39

I tried with first mtree issued file and it still didn't helped

130 root@archiso ~ # grep mtree out.txt| head -1
btop: no mtree file
root@archiso ~ # pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg --dbonly -Sy btop
:: Synchronizing package databases...
 core is up to date
 extra is up to date
warning: btop-1.4.0-4 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...

Packages (1) btop-1.4.0-4

Total Installed Size:  1.56 MiB

:: Proceed with installation? [Y/n]
(1/1) checking keys in keyring                                                                                            [##########################################################################] 100%
(1/1) checking package integrity                                                                                          [##########################################################################] 100%
(1/1) loading package files                                                                                               [##########################################################################] 100%
:: Processing package changes...
ldconfig: File /usr/lib32/libharfbuzz-subset.so.0.61010.0 is empty, not checked.
ldconfig: File /usr/lib32/libharfbuzz-subset.so.0 is empty, not checked.
[...]
ldconfig: File /usr/lib/librubberband.so is empty, not checked.

Mounted root under /mnt

root@archiso ~ # mount | grep '/mnt'
/dev/mapper/myroot on /mnt type ext4 (rw,relatime)

seth · 2024-11-10 16:19:45

That's ok, the first pass will not fix any files on disk and you'll have corrupted libraries on the ldconfig run.
Ignore those and continue w/ the second pass.

pag-r · 2024-11-10 16:27:26

I've tried and result below

root@archiso ~ # pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg -Sy btop
:: Synchronizing package databases...
 core is up to date
 extra is up to date
warning: btop-1.4.0-4 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...

Packages (1) btop-1.4.0-4

Total Installed Size:  1.56 MiB
Net Upgrade Size:      0.00 MiB

:: Proceed with installation? [Y/n]
(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%
:: Processing package changes...
(1/1) reinstalling btop                                                                                                   [##########################################################################] 100%
ldconfig: File /usr/lib32/libharfbuzz-subset.so.0.61010.0 is empty, not checked.
[...]
ldconfig: File /usr/lib/libQt6QuickControls2Universal.so.6.8.0 is empty, not checked.
:: Running post-transaction hooks...
(1/4) Arming ConditionNeedsUpdate...
(2/4) Refreshing PackageKit...
Error connecting: Could not connect: No such file or directory
error: command failed to execute correctly
(3/4) Updating icon theme caches...
(4/4) Updating the desktop file MIME type cache...

Is that correct?

seth · 2024-11-10 16:31:20

There are WAY more packages corrupted than just btop.
libharfbuzz-subset.so is from the harfbuzz package and libQt6QuickControls2Universal.so from qt6-declarative and then there's of course whatever you ellipsed.

The mtree corruptions are broken databases, causing the file collisions, but you need to re-install everything with suspicious package deviations and everything in /usr/lib and /usr/bin is super-suspicous.
In doubt rere-install all packages

pag-r · 2024-11-10 16:45:41

I get it. So I should retry to install all of them in the row? I just thought it's a matter to install one-by-one. Never had such situation, so that's something new to me. When trying to re-reinstall it gives me

 root@archiso ~ # pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg -Qnq | pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg -S -
warning: a52dec-0.8.0-2 is up to date -- reinstalling
[...]
warning: zxing-cpp-2.2.1-1 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...
warning: dependency cycle detected:
warning: pam will be installed before its systemd-libs dependency
warning: dependency cycle detected:
warning: harfbuzz will be installed before its freetype2 dependency
warning: dependency cycle detected:
warning: mesa will be installed before its libglvnd dependency
warning: dependency cycle detected:
warning: nvidia-utils will be installed before its libglvnd dependency
warning: dependency cycle detected:
warning: eglexternalplatform will be installed before its libglvnd dependency
warning: dependency cycle detected:
warning: python-soupsieve will be installed before its python-beautifulsoup4 dependency
warning: dependency cycle detected:
warning: libcamera-ipa will be installed before its libcamera dependency
warning: dependency cycle detected:
warning: qt6-multimedia-ffmpeg will be installed before its qt6-multimedia dependency

Packages (1139) a52dec-0.8.0-2 [...] zxing-cpp-2.2.1-1

Total Installed Size:  9329.42 MiB
Net Upgrade Size:       556.30 MiB

:: Proceed with installation? [Y/n]
xorg-xbacklight: /mnt/usr/share/licenses/xorg-xbacklight/COPYING exists in filesystem
xorg-xbacklight: /mnt/usr/share/man/man1/xbacklight.1.gz exists in filesystem
Errors occurred, no packages were upgraded.

So I guess I completely broke my installation

seth · 2024-11-10 16:49:29

So I guess I completely broke my installation

No. Relax, we get there

You've a conflict in (at least) xorg-xbacklight which you probably want to replace w/ acpilight at some point.
It'll likely also show up w/ a corrupted mtree?

In very doubt re-install all packages --dbonly first, then again w/o --dbonly

pag-r · 2024-11-10 17:17:12

It went much more smooth now.
I guess I can skip multilib now
Output looks like this

mount -t proc proc /mnt/proc; mount --rbind /sys /mnt/sys; mount --rbind /dev /mnt/dev
pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg -Qnq | pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg --dbonly -Sy -
mount /dev/nvme0n1p1 /mnt/boot
pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg -Qnq | pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg -Sy -
[...]
:: Running post-transaction hooks...
( 1/33) Creating system user accounts...
( 2/33) Updating journal message catalog...
( 3/33) Reloading system manager configuration...
  Skipped: Running in chroot.
( 4/33) Reloading user manager configuration...
  Skipped: Running in chroot.
( 5/33) Updating udev hardware database...
( 6/33) Applying kernel sysctl settings...
  Skipped: Running in chroot.
( 7/33) Creating temporary files...
( 8/33) Reloading device manager configuration...
  Skipped: Running in chroot.
( 9/33) Arming ConditionNeedsUpdate...
(10/33) Updating the MIME type database...
(11/33) Rebuilding certificate stores...
(12/33) Updating module dependencies...
(13/33) Restarting cronie for libc upgrade...
Running in chroot, ignoring command 'try-restart'
(14/33) Updating linux initcpios...
==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'default'
==> Using default configuration file: '/etc/mkinitcpio.conf'
  -> -k /boot/vmlinuz-linux -g /boot/initramfs-linux.img
==> Starting build: '6.11.6-arch1-1'
  -> Running build hook: [base]
  -> Running build hook: [udev]
  -> Running build hook: [autodetect]
  -> Running build hook: [modconf]
  -> Running build hook: [kms]
  -> Running build hook: [keyboard]
==> WARNING: Possibly missing firmware for module: 'xhci_pci'
  -> Running build hook: [keymap]
  -> Running build hook: [consolefont]
==> WARNING: consolefont: no font found in configuration
  -> Running build hook: [block]
  -> Running build hook: [lvm2]
  -> Running build hook: [encrypt]
==> WARNING: Possibly missing firmware for module: 'qat_420xx'
  -> Running build hook: [filesystems]
  -> Running build hook: [fsck]
==> Generating module dependencies
==> Creating zstd-compressed initcpio image: '/boot/initramfs-linux.img'
  -> Early uncompressed CPIO image generation successful
==> Initcpio image generation successful
==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'fallback'
==> Using default configuration file: '/etc/mkinitcpio.conf'
  -> -k /boot/vmlinuz-linux -g /boot/initramfs-linux-fallback.img -S autodetect
==> Starting build: '6.11.6-arch1-1'
  -> Running build hook: [base]
  -> Running build hook: [udev]
  -> Running build hook: [modconf]
  -> Running build hook: [kms]
==> WARNING: Possibly missing firmware for module: 'ast'
  -> Running build hook: [keyboard]
==> WARNING: Possibly missing firmware for module: 'xhci_pci'
  -> Running build hook: [keymap]
  -> Running build hook: [consolefont]
==> WARNING: consolefont: no font found in configuration
  -> Running build hook: [block]
==> WARNING: Possibly missing firmware for module: 'qla1280'
==> WARNING: Possibly missing firmware for module: 'aic94xx'
==> WARNING: Possibly missing firmware for module: 'qed'
==> WARNING: Possibly missing firmware for module: 'wd719x'
==> WARNING: Possibly missing firmware for module: 'qla2xxx'
==> WARNING: Possibly missing firmware for module: 'bfa'
  -> Running build hook: [lvm2]
  -> Running build hook: [encrypt]
==> WARNING: Possibly missing firmware for module: 'qat_420xx'
  -> Running build hook: [filesystems]
  -> Running build hook: [fsck]
==> Generating module dependencies
==> Creating zstd-compressed initcpio image: '/boot/initramfs-linux-fallback.img'
  -> Early uncompressed CPIO image generation successful
==> Initcpio image generation successful
(15/33) Refreshing PackageKit...
Error connecting: Could not connect: No such file or directory
error: command failed to execute correctly
(16/33) Updating the appstream cache...
✔ Metadata cache was updated successfully.
(17/33) Reloading system bus configuration...
  Skipped: Running in chroot.
(18/33) Warn about old perl modules
(19/33) Updating fontconfig cache...
(20/33) Updating 32-bit fontconfig cache...
/usr/bin/fc-cache-32: error while loading shared libraries: /usr/lib32/libexpat.so.1: file too short
error: command failed to execute correctly
(21/33) Probing GDK-Pixbuf loader modules...
(22/33) Updating GIO module cache...
(23/33) Compiling GSettings XML schema files...
(24/33) Probing GTK2 input method modules...
(25/33) Probing GTK3 input method modules...
(26/33) Updating icon theme caches...
(27/33) Updating GTK4 module cache...
(28/33) Reloading GVFS config...
(29/33) Updating the info directory file...
(30/33) Updating the desktop file MIME type cache...
(31/33) Updating the vlc plugin cache...
(32/33) Updating Vim help tags...
(33/33) Updating X fontdir indices...

I'm not sure should I worry about PackageKit refreshing?

seth · 2024-11-10 17:23:04

PackageShit won't work in this context, that's no concern
The system should boot and you can try to -Syu from there.

NB. The broken lib32/libexpat.so.1, you probably want to address that.

pag-r · 2024-11-10 17:43:13

It finally worked. Thanks a lot.
As for the lib32 - I'll manage that.
Once again - thanks

Arch Linux

#1 2024-11-10 13:14:07

[Solved] Power loss when upgrading kernel, unable to install packages

#2 2024-11-10 14:36:03

Re: [Solved] Power loss when upgrading kernel, unable to install packages

#3 2024-11-10 16:17:39

Re: [Solved] Power loss when upgrading kernel, unable to install packages

#4 2024-11-10 16:19:45

Re: [Solved] Power loss when upgrading kernel, unable to install packages

#5 2024-11-10 16:27:26

Re: [Solved] Power loss when upgrading kernel, unable to install packages

#6 2024-11-10 16:31:20

Re: [Solved] Power loss when upgrading kernel, unable to install packages

#7 2024-11-10 16:45:41

Re: [Solved] Power loss when upgrading kernel, unable to install packages

#8 2024-11-10 16:49:29

Re: [Solved] Power loss when upgrading kernel, unable to install packages

#9 2024-11-10 17:17:12

Re: [Solved] Power loss when upgrading kernel, unable to install packages

#10 2024-11-10 17:23:04

Re: [Solved] Power loss when upgrading kernel, unable to install packages

#11 2024-11-10 17:43:13

Re: [Solved] Power loss when upgrading kernel, unable to install packages

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