Arch Linux

luckyreveillon

Member

Registered: 2026-01-01

Posts: 2

[SOLVED] Pacman deleted itself misteriously

TLDR: I tried to update, didnt read the output on the terminal window and found that all pacman binaries disappeared from my system. I want to discover what happened

I ran -Syu  (roughly at 19:39) and went afk while it downloaded stuff. The system suspended automatically at 20:14 and some time later I turned it off with the button, without waking it up from suspension beforehand. that is, I didnt read any output on the terminal window.

After booting it up, I noticed that pacman itself had been deleted from my system: there are none of the expected binaries described in the package content list  and nothing relevant (to me...) shows on the log! i cut the log with tail to only include recent activity.

I noticed that the log shows no pacman ativity after 19:42, which makes me guess that the suspension and somewhat improper shutdown didnt cause problems.

cat /var/log/pacman.log | tail -n 68
[2025-12-31T19:02:58-0300] [PACMAN] Running 'pacman -S --needed --noconfirm postgresql'
[2025-12-31T19:03:00-0300] [ALPM] transaction started
[2025-12-31T19:03:01-0300] [ALPM] installed postgresql (18.1-1)
[2025-12-31T19:03:01-0300] [ALPM] transaction completed
[2025-12-31T19:03:01-0300] [ALPM] running '20-systemd-sysusers.hook'...
[2025-12-31T19:03:01-0300] [ALPM-SCRIPTLET] Creating group 'postgres' with GID 938.
[2025-12-31T19:03:01-0300] [ALPM-SCRIPTLET] Creating user 'postgres' (PostgreSQL user) with UID 938 and GID 938.
[2025-12-31T19:03:01-0300] [ALPM] running '30-systemd-daemon-reload-system.hook'...
[2025-12-31T19:03:01-0300] [ALPM] running '30-systemd-tmpfiles.hook'...
[2025-12-31T19:03:02-0300] [ALPM] running '30-systemd-update.hook'...
[2025-12-31T19:16:57-0300] [PACMAN] Running 'pacman -S postgresql-libs'
[2025-12-31T19:38:54-0300] [PACMAN] Running 'pacman -Syu'
[2025-12-31T19:38:54-0300] [PACMAN] synchronizing package lists
[2025-12-31T19:38:56-0300] [PACMAN] starting full system upgrade
[2025-12-31T19:39:28-0300] [PACMAN] Running 'pacman -R -s -n --noconfirm --config /etc/pacman.conf -- google-chrome'
[2025-12-31T19:39:28-0300] [ALPM] transaction started
[2025-12-31T19:39:28-0300] [ALPM] removed google-chrome (143.0.7499.40-1)
[2025-12-31T19:39:28-0300] [ALPM] transaction completed
[2025-12-31T19:39:28-0300] [ALPM] running '30-systemd-update.hook'...
[2025-12-31T19:39:28-0300] [ALPM] running 'gtk-update-icon-cache.hook'...
[2025-12-31T19:39:29-0300] [ALPM] running 'update-desktop-database.hook'...
[2025-12-31T19:39:32-0300] [PACMAN] Running 'pacman -Syu'
[2025-12-31T19:39:32-0300] [PACMAN] synchronizing package lists
[2025-12-31T19:39:32-0300] [PACMAN] starting full system upgrade
[2025-12-31T19:41:56-0300] [ALPM] running '60-mkinitcpio-remove.hook'...
[2025-12-31T19:41:57-0300] [ALPM] running '70-dkms-upgrade.hook'...
[2025-12-31T19:41:58-0300] [ALPM-SCRIPTLET] ==> dkms remove --no-depmod zenpower3/0.2.0 -k 6.17.9-arch1-1
[2025-12-31T19:41:58-0300] [ALPM-SCRIPTLET] ==> dkms remove --no-depmod zenpower3/0.2.0 -k 6.17.9-zen1-1-zen
[2025-12-31T19:42:01-0300] [ALPM] running '71-dkms-remove.hook'...
[2025-12-31T19:42:02-0300] [ALPM] transaction started
[2025-12-31T19:42:02-0300] [ALPM] removed python-proton-vpn-network-manager (0.13.4-2)
[2025-12-31T19:42:02-0300] [ALPM] removed lib32-vulkan-mesa-device-select (1:25.2.7-1)
[2025-12-31T19:42:02-0300] [ALPM] removed vulkan-mesa-device-select (1:25.2.7-1)
[2025-12-31T19:42:02-0300] [ALPM] upgraded adw-gtk-theme (6.3-1 -> 6.4-1)
[2025-12-31T19:42:02-0300] [ALPM] upgraded tzdata (2025b-1 -> 2025c-1)
[2025-12-31T19:42:02-0300] [ALPM] upgraded iana-etc (20251114-1 -> 20251215-1)
[2025-12-31T19:42:02-0300] [ALPM] upgraded readline (8.3.001-1 -> 8.3.003-1)
[2025-12-31T19:42:02-0300] [ALPM] upgraded bash (5.3.8-1 -> 5.3.9-1)
[2025-12-31T19:42:02-0300] [ALPM] upgraded libaec (1.1.4-2 -> 1.1.4-3)
[2025-12-31T19:42:02-0300] [ALPM] upgraded hdf5 (1.14.6-5 -> 2.0.0-3)
[2025-12-31T19:42:02-0300] [ALPM] upgraded alembic (1.8.10-1 -> 1.8.10-2)
[2025-12-31T19:42:03-0300] [ALPM] upgraded alsa-ucm-conf (1.2.14-2 -> 1.2.15.1-1)
[2025-12-31T19:42:03-0300] [ALPM] upgraded alsa-lib (1.2.14-2 -> 1.2.15.1-1)
[2025-12-31T19:42:03-0300] [ALPM] upgraded hwdata (0.401-1 -> 0.402-1)
[2025-12-31T19:42:03-0300] [ALPM] upgraded xz (5.8.1-1 -> 5.8.2-1)
[2025-12-31T19:42:03-0300] [ALPM] upgraded alsa-utils (1.2.14-1 -> 1.2.15.1-1)
[2025-12-31T19:42:03-0300] [ALPM] upgraded amd-ucode (20251125-1 -> 20251125-2)
[2025-12-31T19:42:03-0300] [ALPM] upgraded aom (3.13.1-1 -> 3.13.1-2)
[2025-12-31T19:42:03-0300] [ALPM] upgraded util-linux-libs (2.41.2-1 -> 2.41.3-1)
[2025-12-31T19:42:03-0300] [ALPM] upgraded apache (2.4.65-4 -> 2.4.66-1)
[2025-12-31T19:42:03-0300] [ALPM] upgraded glib2 (2.86.2-1 -> 2.86.3-1)
[2025-12-31T19:42:03-0300] [ALPM] upgraded libgpg-error (1.56-1 -> 1.58-1)
[2025-12-31T19:42:03-0300] [ALPM] upgraded libidn2 (2.3.7-1 -> 2.3.8-1)
[2025-12-31T19:42:03-0300] [ALPM] upgraded systemd-libs (258.2-2 -> 259-1)
[2025-12-31T19:42:03-0300] [ALPM] upgraded libnghttp3 (1.13.1-1 -> 1.14.0-1)
[2025-12-31T19:42:03-0300] [ALPM] upgraded ca-certificates-mozilla (3.118.1-1 -> 3.119.1-1)
[2025-12-31T19:42:03-0300] [ALPM] upgraded gnupg (2.4.8-3 -> 2.4.9-1)
[2025-12-31T19:42:04-0300] [ALPM] upgraded device-mapper (2.03.37-1 -> 2.03.38-1)
[2025-12-31T19:42:04-0300] [ALPM] upgraded cryptsetup (2.8.1-1 -> 2.8.3-1)
[2025-12-31T19:42:04-0300] [ALPM] upgraded util-linux (2.41.2-1 -> 2.41.3-1)
[2025-12-31T19:42:04-0300] [ALPM] warning: /etc/systemd/journald.conf installed as /etc/systemd/journald.conf.pacnew
[2025-12-31T19:42:04-0300] [ALPM] upgraded systemd (258.2-2 -> 259-1)
[2025-12-31T19:42:04-0300] [ALPM-SCRIPTLET] Creating group 'empower' with GID 937.
[2025-12-31T19:42:05-0300] [ALPM-SCRIPTLET] :: This is a systemd feature update. You may want to have a look at
[2025-12-31T19:42:05-0300] [ALPM-SCRIPTLET]    NEWS for what changed, or if you observe unexpected behavior:
[2025-12-31T19:42:05-0300] [ALPM-SCRIPTLET]      /usr/share/doc/systemd/NEWS
[2025-12-31T19:42:05-0300] [ALPM] installed libmakepkg-dropins (18-1)
[2025-12-31T19:42:05-0300] [ALPM] transaction failed

And a search for pacman files:

sudo fd --exclude $(whoami) 'pacman|alpm' /
/var/log/pacman.log
/var/lib/pacman/
/var/lib/pacman/local/pacman-7.1.0.r7.gb9f7d4a-1/
/var/lib/pacman/local/pacman-contrib-1.13.0-1/
/var/lib/pacman/local/pacman-mirrorlist-20251021-1/
/var/lib/pacman/local/ALPM_DB_VERSION
/usr/share/doc/qt/examples/script/context2d/scripts/pacman.js
/usr/share/vim/vim91/syntax/pacmanlog.vim
/usr/share/fish/completions/pacman-color.fish
/usr/share/fish/completions/pacman-key.fish
/usr/share/fish/completions/pacman.fish
/usr/share/fish/functions/__fish_print_pacman_packages.fish
/usr/share/fish/functions/__fish_print_pacman_repos.fish
/usr/share/nvim/runtime/syntax/pacmanlog.vim
/usr/share/libalpm/
/usr/share/pacman/
/usr/share/swcatalog/icons/archlinux-arch-extra/64x64/pacman-offline_system-software-update.png
/usr/share/swcatalog/icons/archlinux-arch-extra/64x64/pacmanlogviewer_plv.png
/usr/share/swcatalog/icons/archlinux-arch-extra/128x128/pacman-offline_system-software-update.png
/usr/share/swcatalog/icons/archlinux-arch-extra/128x128/pacmanlogviewer_plv.png
/usr/share/swcatalog/icons/archlinux-arch-extra/48x48/pacman-offline_system-software-update.png
/usr/share/swcatalog/icons/archlinux-arch-extra/48x48/pacmanlogviewer_plv.png
/usr/lib/systemd/system/pacman-filesdb-refresh.timer
/usr/lib/systemd/system/pacman-filesdb-refresh.service
/var/cache/pacman/
/var/lib/flatpak/appstream/flathub/x86_64/a865e85f767056848301f54557098fb44416bf8dc8ec57441a0268eb957b1e1b/icons/64x64/it.cuteworks.pacmanlogviewer.png
/etc/conf.d/pacman-contrib
/etc/pacman.d/
/etc/pacman.conf
/etc/pacman.conf.pacnew
/var/lib/flatpak/appstream/flathub/x86_64/a865e85f767056848301f54557098fb44416bf8dc8ec57441a0268eb957b1e1b/icons/128x128/it.cuteworks.pacmanlogviewer.png

Also, my pacman cache is gone, maybe due to a symlink misconfig on my end.
the system is otherwise functional and I know I can try downloading and untaring the package directly into my / to at least get pacman back, but I havent tried that yet to avoid losing any info that could help me figure out what caused this

Last edited by luckyreveillon (2026-01-01 17:37:45)

Scimmia

Fellow

Registered: 2012-09-01

Posts: 13,723

Re: [SOLVED] Pacman deleted itself misteriously

Also, my pacman cache is gone, maybe due to a symlink misconfig on my end.

Yes, that's actually the entire problem, and covered here: https://wiki.archlinux.org/title/Pacman … _not_found

The next section under that (3.7) tells you how to fix it.

Last edited by Scimmia (2026-01-01 17:13:14)

5hridhyan

Member

From: Asia

Registered: 2025-12-25

Posts: 648

Re: [SOLVED] Pacman deleted itself misteriously

no not "misteriously", like you said

The system suspended automatically and later I turned it off with the button, without waking it up.

it happens when you do partial upgrades or like interrupting during an active pacman transaction.

Last edited by 5hridhyan (2026-01-01 17:28:59)

---

"Nothing matters" -a Nihilist
"Why bother thinking what matters?" -me

Scimmia

Fellow

Registered: 2012-09-01

Posts: 13,723

Re: [SOLVED] Pacman deleted itself misteriously

or like interrupting during an active pacman transaction.

The transaction failed long before that.

5hridhyan

Member

From: Asia

Registered: 2025-12-25

Posts: 648

Re: [SOLVED] Pacman deleted itself misteriously

The transaction failed long before that.

Sorry I missed that.

Last edited by 5hridhyan (2026-01-01 18:42:28)

---

"Nothing matters" -a Nihilist
"Why bother thinking what matters?" -me

luckyreveillon

Member

Registered: 2026-01-01

Posts: 2

Re: [SOLVED] Pacman deleted itself misteriously

Also, my pacman cache is gone, maybe due to a symlink misconfig on my end.

Yes, that's actually the entire problem, and covered here: https://wiki.archlinux.org/title/Pacman … _not_found

The next section under that (3.7) tells you how to fix it.

Ouch, I hadnt seen that section and kinda assumed it was some sort of bug. Thanks!