Pacman and paru databases out of sync?

When I do sudo pacman -Syu, I get a list of currently 29 packages.

But paru -Syu yields nothing?!

paru -Syu
:: Looking for devel upgrades...
:: packages not in the AUR: kinit
:: marked out of date: epsonscan2
 there is nothing to do

So I asked Perp for assistance and it tells me to:

  • Clear Paru cache: paru -Sc then retry paru -Syu. (hc4a: didn’t do that yet)
  • Check differences: pacman -Qu vs paru -Qua to see repo vs AUR/outdated packages. (hc4a: paru -Qua yields nothing while pacman gives the 29 pkgs)
  • Full update flow: pacman -Syu first, then paru -Su --needed for AUR (hc4a: didn’t do that yet)

Earlier it told me to check if pacman -Syyu and paru -Syyu would differ, too (which they do) and also to count the entries in both databases:

╰─> ls -la /var/lib/pacman/sync/*.db | wc -l
7

╰─> ls -la /var/lib/paru/sync/*.db | wc -l
zsh: no matches found: /var/lib/paru/sync/*.db
0

So now I wonder:

  1. Where might this behavior stem from? I just recently had the weird case that my mirrorlist seem to have disappeared. Could this be related?
  2. What do I actually need to do in order to fix this?
  3. How can I prevent this in the future?

PS: I also wonder about the epsonscan2 being “out of date”, but that may be related, right?

I was under the impression that paru simply used pacman as a backend, in which case this doesn’t make sense (so I must be wrong?)

Yep, it’s a live-and-learn moment for me too :sweat_smile: Maybe the “info” about /var/lib/paru/sync/*.db is also wrong, I dunno.

PS: I just learned you can format code with Ctrl+E :slight_smile:

It is.

I dont know how we ended up here .. but thats not a path that should normally exist.

Maybe we can also wonder about the paru that is in use?

Something like;

pacman -Qi paru

That is the question.
Its not just normal paru behavior.
And I cannot find something like a relevant flag for this or any mention in the man pages.

Maybe just delete these weird paths and wipe out any local paru config that is set as such? (~/.config/paru/*.conf)

Again part of the mystery.
Assuming its not some off-brand paru that is innately funky then we must assume it was some action (so dont do that again)?

Maybe following something like this?;
https://www.reddit.com/r/archlinux/comments/tkeuy5/using_paru_u_chroot_to_build_a_pkgbuild_in_a/

:thinking:

It was Perplexity who asked me to check /var/lib/paru/sync/*.db, so I file that under hallucinations and there is no such weird path at all. But also no ~./config/paru directory:

╰─> ls -la /var/lib/paru/sync/            
ls: cannot access '/var/lib/paru/sync/': No such file or directory

╰─> ls -la ~./config/paru      
ls: cannot access '/home/hc4a/.config/paru': No such file or directory

Here is pacman -Qi paru:

Installed From  : cachyos
Name            : paru
Version         : 2.1.0-2
Description     : Feature packed AUR helper
Architecture    : x86_64
URL             : https://github.com/morganamilo/paru
Licenses        : GPL-3.0-or-later
Groups          : None
Provides        : None
Depends On      : git  pacman  libalpm.so>=14
Optional Deps   : bat: colored pkgbuild printing [installed]
                  devtools: build in chroot and downloading pkgbuilds
Required By     : None
Optional For    : cachy-update  octopi
Conflicts With  : None
Replaces        : None
Installed Size  : 7.85 MiB
Packager        : CachyOS <admin@cachyos.org>
Build Date      : Sun 09 Nov 2025 11:55:03 PM CET
Install Date    : Wed 17 Dec 2025 02:55:06 PM CET
Install Reason  : Explicitly installed
Install Script  : No
Validated By    : Signature

I assure you I did not do anything by myself (Edit: yes, I did :weary_face: ), I actually hardly use paru. My history reveals that the last paru things were:

 2717  paru -S linux-cachyos linux-cachyos-headers linux-cachyos-nvidia-open --rebuild 
 2720  paru -S linux-cachyos linux-cachyos-headers linux-cachyos-nvidia-open --rebuild 
 2724  paru -S linux-cachyos linux-cachyos-headers linux-cachyos-nvidia-open --rebuild
 2726  paru -S linux-cachyos linux-cachyos-headers cachyos-znver4/linux-cachyos-nvidia-open --rebuild
 2727  paru -S linux-cachyos linux-cachyos-headers
 2732  paru -S linux-cachyos linux-cachyos-headers
 3104  tldr paru
 3105  paru -Rns anydesk-bin

with those 27xx entries most likely been done by cachy-update :thinking:

Now what? How can this be:

╰─> checkupdates            
ark 25.12.3-1.1 -> 26.04.0-1.1
baloo-widgets 25.12.3-1.1 -> 26.04.0-1.1
cups 2:2.4.16-2 -> 2:2.4.17-1
cups-pdf 3.0.2-1.7 -> 3.0.2-1.8
dolphin 25.12.3-1.1 -> 26.04.0-1.1
ffmpegthumbs 25.12.3-1.1 -> 26.04.0-1.1
filelight 25.12.3-1.1 -> 26.04.0-1.1
gwenview 25.12.3-1.1 -> 26.04.0-1.1
kaccounts-integration 25.12.3-1.1 -> 26.04.0-1.1
kate 25.12.3-1.1 -> 26.04.0-1.1
kcalc 25.12.3-1.1 -> 26.04.0-1.1
kcharselect 25.12.3-1.1 -> 26.04.0-1.1
kdeconnect 25.12.3-1.1 -> 26.04.0-1.1
kdegraphics-mobipocket 25.12.3-1.1 -> 26.04.0-1.1
kdegraphics-thumbnailers 25.12.3-1.1 -> 26.04.0-1.1
kdialog 25.12.3-1.1 -> 26.04.0-1.1
kio-admin 25.12.3-1.1 -> 26.04.0-1.1
kio-extras 25.12.3-1.1 -> 26.04.0-1.1
kompare 25.12.3-1.1 -> 26.04.0-1.1
konsole 25.12.3-1.1 -> 26.04.0-1.1
kpmcore 25.12.3-1.1 -> 26.04.0-1.1
kwalletmanager 25.12.3-1.1 -> 26.04.0-1.1
libcups 2:2.4.16-2 -> 2:2.4.17-1
libcupsfilters 2.1.1-4.1 -> 2.1.1-4.2
libjcat 0.2.5-1.2 -> 0.2.6-1.1
libkdcraw 25.12.3-2 -> 26.04.0-1
libkexiv2 25.12.3-1.2 -> 26.04.0-1.1
libkomparediff2 25.12.3-1.1 -> 26.04.0-1.1
libmysofa 1.3.3-1.1 -> 1.3.4-1.1
openexr 3.4.9-2.1 -> 3.4.10-1.1
partitionmanager 25.12.3-1.1 -> 26.04.0-1.1
python-lxml 6.0.4-1.1 -> 6.1.0-1.1
signon-kwallet-extension 25.12.3-1.1 -> 26.04.0-1.1
wine 11.6-1.1 -> 11.7-1.1

but

╰─> paru -Syu      
:: Looking for devel upgrades...
:: packages not in the AUR: kinit
:: marked out of date: epsonscan2
 there is nothing to do

:worried:

Ah. Well then the weird extra db thing wasnt real. :sweat_smile:
That path was the reason for the bulk of my response above..

As to

If you dont have a conf in $HOME then maybe check the one at /etc/paru.conf?

Given your output I might wonder if you have set something like AurOnly.

( Which, to be fair, would not be a bad setup. I tend to keep things separated and use pacman with paru only for the AUR. The explicit locked config I could take or leave really. )

╰─> cat /etc/paru.conf          
#
# $PARU_CONF
# /etc/paru.conf
# ~/.config/paru/paru.conf
#
# See the paru.conf(5) manpage for options

#
# GENERAL OPTIONS
#
[options]
PgpFetch
Devel
Provides
DevelSuffixes = -git -cvs -svn -bzr -darcs -always -hg -fossil
AurOnly
BottomUp
#RemoveMake
#SudoLoop
#UseAsk
#SaveChanges
#CombinedUpgrade
#CleanAfter
#UpgradeMenu
#NewsOnUpgrade

#LocalRepo
#Chroot
#Sign
#SignDb
#KeepRepoCache

#
# Binary OPTIONS
#
#[bin]
#FileManager = vifm
#MFlags = --skippgpcheck
#Sudo = doas

Yes, looks like. But why? And how should the paru.conf look like? Am I supposed to alter that file in /etc at all?

Edit: aah… wait… I’ll check my diary on that… gimme a sec.

I dont know why you did it exactly, but I dont think thats the default.

But the reason I would do it would be to ensure the aur helper was only used for the AUR.

I know lots of folks on here tend to like firing paru as a catch-all solution but I’m more old-school and like pacman for the repos and aur helpers for their one purpose. ex;

sudo pacman -Syu && paru -Sua

That option would be in line with that kind of thinking.

So yeah, my diary reveals that I actually did that:

  1. So konfigurieren, dass paru sich nur um AUR packages kümmert:
    /etc/paru.conf:
    AurOnly

:sweat_smile:

Mystery resolved. Thanks once again, @cscs. When we meet next time, remind me I owe you a beer (or two).

That only leaves me with the question why this is:

╰─> paru -Syu      
:: Looking for devel upgrades...
:: packages not in the AUR: kinit
:: **marked out of date: epsonscan2**

Does that mean this package is not being maintained any longer? Or is this any okayish state?

Yeah that means kinit is not in the AUR (after already not being in the repos).

So it can be called a ‘super-alien’ of sorts.

If you dont have some known compelling reason to be keeping it and/or werent manually maintaining/installing it with some purpose .. if its just some old package .. then its been deprecated for how ever long and should probably be removed.

PS.

As to the epsonscan2 package message it means someone flagged the AUR package as out of date. It usually means it will be updated shortly.

Will do right now. And thanks for the info on epsonscan, I’ll try to keep that in mind and look for it every now and again.

Edit: apparently, I installed that explicitely?

╰─> pacman -Qi kinit 
Installed From  : cachyos-extra-znver4
Name            : kinit
Version         : 5.116.0-1.1
Description     : Process launcher to speed up launching KDE applications
Architecture    : x86_64_v4
URL             : https://community.kde.org/Frameworks
Licenses        : LGPL
Groups          : kf5
Provides        : None
Depends On      : kio5
Optional Deps   : None
Required By     : None
Optional For    : None
Conflicts With  : None
Replaces        : None
Installed Size  : 505.72 KiB
Packager        : CachyOS <admin@cachyos.org>
Build Date      : Sun 09 Jun 2024 10:32:06 PM CEST
Install Date    : Mon 02 Jun 2025 12:51:04 PM CEST
Install Reason  : Explicitly installed
Install Script  : Yes
Validated By    : Signature

I am losing track on my system :sweat_smile: My diary has nothing on kinit. Off it goes.

Nothing really for you to do.

Someone in the community flagged the PKGBUILD (etc) as needing updates. Probably some user noticed a newer version is available but the AUR package has not been changed to reflect it. Anyone can do this. And it is supposed to indicate that the maintainer needs to do something. If or when they do then you will get an update to the AUR package.

Its probably not the shortest list but not monstrous either;

pacman -Qet

That will print explicitly installed packages not needed by anything else.
I would not probably say they are all safe to remove .. but it would be a list to review.
( To find some packages in it that maybe you forgot about installing. )

Hahaha nope nope nope, I need one or the other of those packages :rofl:

╰─> pacman -Qet
alacritty 0.17.0-1.1
alsa-firmware 1.2.4-4
alsa-utils 1.2.15.2-2.1
amd-ucode 1:20260309-1
ark 25.12.3-1.1
audacious 4.5.1-1.1
awesome-terminal-fonts 1.1.0-5
base 3-3
blueman 2.4.6-2.1
bluez-hid2hci 5.86-5.1
bluez-utils 5.86-5.1
btop 1.4.6-2.1
btrfs-assistant 2.2-5.1
cachy-update 3.19.1-1
cachyos-fish-config 15-1
cachyos-hello 0.23.2-1
cachyos-hooks 2026.02.05-1
cachyos-iridescent-kde r2.16aa352-1
cachyos-kde-settings 4.9-8
cachyos-kernel-manager 1.17.0-1
cachyos-keyring 20240331-1
cachyos-micro-settings 1.0.0-1
cachyos-mirrorlist 27-1
cachyos-nord-kde-theme-git r16.d75759c-1
cachyos-packageinstaller 1.6.2-1
cachyos-plymouth-theme 1-1
cachyos-rate-mirrors 23-1
cachyos-snapper-support 1.0.2-1
cachyos-themes-sddm 1.0-3
cachyos-v3-mirrorlist 27-1
cachyos-v4-mirrorlist 27-1
cachyos-zsh-config 1.0.3-1
cowsay 3.8.4-1
cpupower 7.0-3
cups-pdf 3.0.2-1.7
dmraid 1.0.0.rc16.3-15.1
dolphin 25.12.3-1.1
downgrade 12.0.1-1
duf 0.9.1-1.1
easytag 2.4.3-16.1
efitools 1.9.2-7.1
epsonscan2 6.7.82.0-1
etcher-bin 2.1.4-1
ethtool 1:6.19-1.1
ex-vi-compat 2-1
ffmpegthumbnailer 2.3.0-1.2
filezilla 3.70.1-1.1
firefox 149.0.2-1.1
foomatic-db-engine 5:20200131-2.1
foomatic-db-nonfree 3:20260209-1
fsarchiver 0.8.9-1.1
gimp 3.2.2-1
glances 4.5.3.2-1
gparted 1.8.1-1.1
grsync 1.3.1-2.1
gsfonts 20200910-6
guvcview 2.2.2-1.1
gwenview 25.12.3-1.1
gxplugins.lv2 1.0-3.1
haruna 1.7.1-2.1
haveged 1.9.19-1.1
hdparm 9.65-3.1
htop 3.5.0-1.1
hugin 2025.0.1-4.1
hunspell-de 20161207-9
hunspell-en_gb 2026.02.25-1
hwdetect 2025.08.16.1333-1
hwinfo 25.2-1.1
inetutils 2.7-2.1
inkscape 1.4.3-8.1
innoextract 1.9-15.1
kate 25.12.3-1.1
kcalc 25.12.3-1.1
kcharselect 25.12.3-1.1
kde-gtk-config 6.6.4-1.1
kdeplasma-addons 6.6.4-1.1
kid3 3.9.7-2.5
kinit 5.116.0-1.1
krename 5.0.2-11.1
kwallet-pam 6.6.4-1.1
libgsf 1.14.56-1.1
libreoffice-fresh 26.2.2-3.1
libva-nvidia-driver 0.0.16-1.2
libwnck3 43.3-1.3
linux-cachyos-headers 7.0.0-1
linux-cachyos-lts-headers 6.18.22-1
linux-cachyos-lts-nvidia-open 6.18.22-1
linux-cachyos-nvidia-open 7.0.0-1
lsscsi 0.32-2.1
man-pages 6.17-1
meld 3.22.3-2
nano-syntax-highlighting 2025.07.01.r0.g256995b-2
netctl 1.29-2
networkmanager-openvpn 1.12.5-1.1
nfs-utils 2.9.1-1.1
noto-color-emoji-fontconfig 1.0.0-2
ntp 4.2.8.p18-6
nvme-cli 2.16-2
obs-studio 32.1.1-2.1
octopi 0.18.1-2
opendesktop-fonts 1.4.2-7
opensnitch 1.7.2-4.1
partitionmanager 25.12.3-1.1
pavucontrol 1:6.2-1.1
plasma-browser-integration 6.6.4-1.1
plasma-firewall 6.6.4-1.1
plasma-systemmonitor 6.6.4-1.1
plasma-thunderbolt 6.6.4-1.1
profile-sync-daemon 1:7.03-1
proton-cachyos 1:10.0.20260408-1
pv 1.10.5-1.1
qt6-wayland 6.11.0-1.1
rebuild-detector 4.4.5-1
refind-btrfs 0.6.5-2
reflector 2023-5
sddm-kcm 6.6.4-1.1
sg3_utils 1.48-1.2
shotcut 26.2.26-1.1
signal-desktop 8.7.0-1
sof-firmware 2025.12.2-1
spectacle 1:6.6.4-1.1
splix 2.0.1-2.1
system-config-printer 1.5.18-6
thunderbird 149.0.2-1.1
ttf-opensans 3.003-1
veracrypt 1.26.24-2.2
vscodium 1.112.01907-1
winetricks 20260125-1.1
xf86-video-amdgpu 25.0.0-1.1
xl2tpd 1.3.20-1.1
xorg-xinit 1.4.4-1.1
xorg-xinput 1.6.4-2.1
xorg-xkill 1.0.7-1.1

I start to wonder whether something about my pacman is seriously borked.

Yeah exactly .. its not an ‘uninstall’ list.

Its a list of

  • Explicitly installed packages.
  • That are also not needed by anything else.

It just may contain some packages worth considering for removal or remembering you dont need or similar. The majority will likely be ones you want to keep.

Something like kinit for example would have been printed here if it had not already been removed.

While something like base obviously is a must have.

Yet it is required by none. Okay, well, Arch is still over my head :laughing: I’ll kick kinit and see what comes next :slight_smile:

It may be illustrative to point out that explicitly installed packages (and especially for our purposes here ones not required by anything else) cannot be orphans.

So something like kinit that would have otherwise been an orphan thrice over three months or more ago .. it languished due to being explicitly installed at some point.

Orphans (pacman -Qdt) should be reviewed but more default to being unneeded (or needing other management to remove the orphan status).

While the list above (pacman -Qet) can be reviewed from time to time to check for any forgotten leftovers. That one package we installed on a whim that one time. But we more default to them being needed - most of them ostensibly being explicitly installed for a reason.

No oprhans sticking around :upside_down_face:

So something like kinit that would have otherwise been an orphan thrice over three months or more ago .. it languished due to being explicitly installed at some point.

I believe it was Cachy itself installing all these things on initial installation in June 2025. Because sure, I installed a lot of those like filezilla and kid3, but most of those packages come from the Cachy installation.

Yes a good chunk of explicitly installed packages may derive from the original install (like base).

But of course those deprecate too.

:weary_face:

“With great power” and all that :sweat_smile: I’m off to Steam to forget about these things for a while now :laughing: