System update failed

yt87 · 5 October 2023 18:49

I recently reinstalled Manjaro on a new drive. No issues until I tried to run the recent update. Here is relevant fragment of pacman.log:

[2023-10-05T18:19:37+0000] [PAMAC] synchronizing package lists
[2023-10-05T18:22:58+0000] [PACMAN] Running 'pacman -Syu'
[2023-10-05T18:22:58+0000] [PACMAN] synchronizing package lists
[2023-10-05T18:23:30+0000] [ALPM] transaction started
[2023-10-05T18:23:30+0000] [ALPM] upgraded archlinux-keyring (20230821-2 -> 20230918-1)
[2023-10-05T18:23:30+0000] [ALPM-SCRIPTLET] ==> Appending keys from archlinux.gpg...
[2023-10-05T18:23:32+0000] [ALPM-SCRIPTLET] ==> Disabling revoked keys in keyring...
[2023-10-05T18:23:32+0000] [ALPM-SCRIPTLET]   -> Disabled 2 keys.
[2023-10-05T18:23:32+0000] [ALPM-SCRIPTLET] ==> Updating trust database...
[2023-10-05T18:23:33+0000] [ALPM-SCRIPTLET] gpg: marginals needed: 3  completes needed: 1  trust model: pgp
[2023-10-05T18:23:33+0000] [ALPM-SCRIPTLET] gpg: depth: 0  valid:   1  signed:  21  trust: 0-, 0q, 0n, 0m, 0f, 1u
[2023-10-05T18:23:33+0000] [ALPM-SCRIPTLET] gpg: depth: 1  valid:  21  signed:  96  trust: 0-, 0q, 0n, 21m, 0f, 0u
[2023-10-05T18:23:33+0000] [ALPM-SCRIPTLET] gpg: depth: 2  valid:  72  signed:  27  trust: 72-, 0q, 0n, 0m, 0f, 0u
[2023-10-05T18:23:33+0000] [ALPM-SCRIPTLET] gpg: next trustdb check due at 2023-10-27
[2023-10-05T18:23:33+0000] [ALPM] transaction completed
[2023-10-05T18:23:33+0000] [ALPM] running '30-systemd-daemon-reload.hook'...
[2023-10-05T18:23:34+0000] [ALPM] running '30-systemd-update.hook'...
[2023-10-05T18:23:34+0000] [ALPM] running '90-packagekit-refresh.hook'...
[2023-10-05T18:23:34+0000] [PACMAN] starting full system upgrade
[2023-10-05T18:24:50+0000] [ALPM] running '60-mkinitcpio-remove.hook'...
[2023-10-05T18:24:50+0000] [ALPM] running '71-dkms-remove.hook'...
[2023-10-05T18:24:50+0000] [ALPM] transaction started
[2023-10-05T18:24:50+0000] [ALPM] error: problem occurred while upgrading filesystem
[2023-10-05T18:24:50+0000] [ALPM] upgraded filesystem (2023.09.03-1 -> 2023.09.22-1)
[2023-10-05T18:24:50+0000] [ALPM] transaction failed

Output from inxi:

CPU: 12-core AMD Ryzen 9 5900X (-MT MCP-) speed/min/max: 2673/2200/4950 MHz
Kernel: 6.5.3-1-MANJARO x86_64 Up: 6d 18h 1m Mem: 10.9/62.68 GiB (17.4%)
Storage: 12.74 TiB (50.3% used) Procs: 496 Shell: Zsh inxi: 3.3.30

The log does not tell where to look for the cause of failure, or the second last line is misleading. Although filesystem seems to be updated:

[asok log]#  pacman -Q filesystem       
filesystem 2023.09.22-1

I need help.

yt87 · 5 October 2023 19:02

Hopefully relevant output from journalctl:

Oct 05 18:38:26 asok archlinux-keyring-wkd-sync[813906]: Refreshing key 5E6D49448958B384301F1F22498EF247>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[814255]: gpg: error retrieving 'fabiscafe@archlinux.org'>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[814255]: gpg: error reading key: End of file
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key 02FD1C7A934E614545849F19A6>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key 169704C6FB490C6892C7F23C37>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key 42DFAFB7C03B2E4E7BBDBA6993>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key 8E1992167465DB5FB045557CB0>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key 954A3772D62EF90E4B31FBC6C9>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key 9D74DF6F91B7BDABD5815CA84A>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key ADC8A1FCC15E01D45310419E94>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key B4B759625D4633430B74877059>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key B81B051F2D7FC867AAFF35A58D>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key BE2DBCF2B1E3E588AC325AEAA0>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key C521846436D75A3294795B27B4>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key CB33B736591A9CA06098A9A5FC>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key D89FAAEB4CECAFD199A2F5E612>
Oct 05 18:38:28 asok archlinux-keyring-wkd-sync[813906]: Error refreshing key 5E6D49448958B384301F1F2249>
Oct 05 18:38:28 asok systemd[1]: archlinux-keyring-wkd-sync.service: Main process exited, code=exited, s>
Oct 05 18:38:28 asok systemd[1]: archlinux-keyring-wkd-sync.service: Failed with result 'exit-code'.
Oct 05 18:38:28 asok systemd[1]: archlinux-keyring-wkd-sync.service: Consumed 1.521s CPU time.
Oct 05 18:38:28 asok pamac-tray-plas[1231]: updates_checker.vala:71: check updates
Oct 05 18:38:30 asok pamac-tray-plas[1231]: updates_checker.vala:101: 95 updates found
Oct 05 18:38:42 asok systemd[1]: Started Process Core Dump (PID 814333/UID 0).
Oct 05 18:38:42 asok systemd-coredump[814334]: [🡕] Process 814332 (eglinfo) of user 501 dumped core.

megavolt · 5 October 2023 19:26

@yt87 Do you have enough space on your root partition?

df -h

yt87 · 5 October 2023 19:44

Yes:

[asok log]# df -h
Filesystem      Size  Used Avail Use% Mounted on
dev              32G     0   32G   0% /dev
run              32G  4.4M   32G   1% /run
efivarfs        128K   36K   88K  29% /sys/firmware/efi/efivars
/dev/nvme1n1p3  269G   15G  241G   6% /
tmpfs            32G   53M   32G   1% /dev/shm
/dev/sdb1       916G  141G  729G  17% /mnt/sdb1
/dev/nvme0n1p1  916G  480G  390G  56% /mnt/nvme0
/dev/sdc1       3.6T  1.6T  1.9T  45% /mnt/sdc1
/dev/sdd1       2.8T  2.1T  717G  75% /mnt/sdd1
tmpfs            32G  4.3G   28G  14% /tmp
/dev/nvme1n1p1  300M  288K  300M   1% /boot/efi
tmpfs           6.3G  112K  6.3G   1% /run/user/501
/dev/sda2       432G   37G  389G   9% /mnt/sda2
/dev/sde1       3.6T  2.2T  1.3T  65% /run/media/george/snapshots

megavolt · 5 October 2023 19:54

sudo pacman-mirrors --geoip
sudo pacman-mirrors --fasttrack
sudo pacman -Syyuu --overwrite "*"

yt87 · 5 October 2023 20:14

Thanks, that worked! I am a bit concerned about this:

Generating grub configuration file ...
Found theme: /usr/share/grub/themes/manjaro/theme.txt
Found linux image: /boot/vmlinuz-6.5-x86_64
Found initrd image: /boot/amd-ucode.img /boot/initramfs-6.5-x86_64.img
Found initrd fallback image: /boot/initramfs-6.5-x86_64-fallback.img
Warning: os-prober will be executed to detect other bootable partitions.
Its output will be used to detect bootable binaries on them and create new boot entries.
Found Manjaro Linux on /dev/sda2
Adding boot menu entry for UEFI Firmware Settings ...
Root filesystem isn't btrfs
If you think an error has occurred, please file a bug report at "https://github.com/Antynea/grub-btrfs"
Found memtest86+ image: /boot/memtest86+/memtest.bin
/usr/bin/grub-probe: warning: unknown device type nvme1n1.
Found memtest86+ EFI image: /boot/memtest86+/memtest.efi
/usr/bin/grub-probe: warning: unknown device type nvme1n1.
done
(17/22) Reloading system bus configuration...

The sda drive is my old Manjaro system disk, which is btrfs while nvme1n1p1 is ext4. The final test will be reboot.

cscs · 5 October 2023 20:18

yt87:

Thanks, that worked! I am a bit concerned about this:

Generating grub configuration file ...
Found theme: /usr/share/grub/themes/manjaro/theme.txt
Found linux image: /boot/vmlinuz-6.5-x86_64
Found initrd image: /boot/amd-ucode.img /boot/initramfs-6.5-x86_64.img
Found initrd fallback image: /boot/initramfs-6.5-x86_64-fallback.img
Warning: os-prober will be executed to detect other bootable partitions.
Its output will be used to detect bootable binaries on them and create new boot entries.
Found Manjaro Linux on /dev/sda2
Adding boot menu entry for UEFI Firmware Settings ...
Root filesystem isn't btrfs
If you think an error has occurred, please file a bug report at "https://github.com/Antynea/grub-btrfs"
Found memtest86+ image: /boot/memtest86+/memtest.bin
/usr/bin/grub-probe: warning: unknown device type nvme1n1.
Found memtest86+ EFI image: /boot/memtest86+/memtest.efi
/usr/bin/grub-probe: warning: unknown device type nvme1n1.
done

Why concerned?
This is the output of update-grub.

Normal.

Since you said you have an extra install on sda … this is also normal.

You said your root should be ext4 … and you are still using grub-btrfs … so normal as well.

At least for me, on an nvme with an ESP formatted fat32 (used by windoze as well) this message is also displayed every update-grub. It also gets a rating of normal.

Yochanan · 5 October 2023 20:34

Warning: Generally avoid using the --overwrite switch. See System maintenance#Avoid certain pacman commands.

– pacman - ArchWiki

megavolt · 5 October 2023 20:37

Alright. Next time…

it should only be used when explicitly recommended by the Arch developers.

yt87 · 5 October 2023 20:38

I see that the package grub-btrfs is installed, even if I did not want a btrfs filesystem. I am not sure it is worthwhile to uninstall it. It is likely another layer that falls back to ext4 in absence of btrfs.

cscs · 5 October 2023 20:41

Yeah thats how the install goes.
I noticed a handful of packages that were unneeded or incorrect given the choices … cronie, timeshift things, and this being among the examples.
Though - since the installs are not dynamic … it makes sense it is like this.

Anyhoo, yes, if you dont use btrfs you can uninstall grub-btrfs - just make sure to have regular grub installed.

system · 8 October 2023 10:42

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