To be honest, this negates the point of a graphical tool - for me, the attraction of Pamac is that it shows a list of everything available and can include repos, aur, flatpaks and the jury’s still out whether anyone uses snap or not…
Though I never use the graphical tool for updates personally, it’s annoying that it seems to bring fragmentation to the table.
I think the problem here, really, is these GUI tools like Pamac seem to combine system package upgrades with those from the AUR in a less-than-ideal way.
My opinion is that these should always be kept separate, making sure the system is up-to-date first. And, preferably, being on the unstable branch, if using AUR-sourced software.
This sounds correct - but is there any reason that it can’t be managed, separately, within the Pamac GUI?
You know - like a ‘topgrade’ thing - do the system update first, followed by AUR, then Flatpak, then Snapd…
I know that Pamac developer has followed the demands from the users - and created a swiss armyknife.
But with swiss armknifes - one use only one tool at a time - if you use two or more simultanously - then you are in trouble.
It is well known that you should not use all pamac’s tool in one transaction
I had this recently also that it stuck at 90% (i had to wait few minutes), for the first time but i could solved it with refreshing my mirrors… thats it.
Pamac was mostly running total fine for my 2 systems. 
Global mirrors and only two?
Go in Pamac preferences and choose your country. And also refresh your mirrors again after that with:
sudo pacman-mirrors --fasttrack
Btw. there are brand new updates around pamac just available, probably helps too.
Exactly my thoughts. 
If making a package manager interface, at least make it do things in the right order.
Oh, and as @Kobold mentioned, only two mirrors.
I’d at least do sudo pacman-mirrors -c Germany or something.
i chose those mirrors for being HTTPS and from a trusted source.
choosing by my region gives countries i don’t trust(no offense).
also that’s always been the case and i had no issues until recently.
i disabled AUR and will check manually from time to time after it’s clear that the system is up to date.
Hi @linub ,
I wonder whether you could read the last two post in the following link, in order to solve the problem.
‘[Stable Update] 2024-10-10 - Kernels, Pacman 7.0, KDE Frameworks 6.6, Virtualbox 7.1.2, Mesa - #195 by Daniel-I’
Hope it help,
Regards
Hello
my issue is currently solved and to be frank i’d rather not touch anything right now.
if it arises again i’ll keep this solution in mind.
Thanks.
If pamac GUI preferences has Enable AUR support enabled, but Check for Updates is turned off, AUR packages can be installed from GUI, but GUI will update repository packages only
AUR packages can be updated with pamac update --aur, but some AUR packages might fail to build if there is a missing dependency on Testing branch. I use pamac build to rebuild packages individually if there is such an issue
You should install the repository packages for Pamac, and NOT Pamac from the AUR that makes absolutely no sense to use the AUR version on Manjaro. It adds a layer of trouble. Use Pacman to reinstall Pamac packages.
my Pamac is not from the AUR,
i only intalled Vmware and Sype from there.
at some point it showed as if it was from there but that was an error when everything got confused.
If Check for Updates is enabled in pamac GUI preferences, Stable branch users are likely to get packages from repository updated to AUR
Branch compare for Manjaro
pamac-cli - stable:11.7.0-0
AUR - pamac-cli
Package Details: pamac-cli 11.7.0-1
When pamac “got confused” it was showing package version of pamac-cli from AUR,
just before you turned off option to check for AUR updates
indeed,so how come this is normal,
wouldn’t this cause issues for users that have AUR+updates enabled,
or a difference in packages versions?
and what would have happened if i did update to pamac-cli 11.7.0-1?
A couple days ago, Pamac (gui version) was causing some kind of memory leak and locking up the whole system when i click on it. I deleted its cache and removed, reinstalled it to no avail. Then i just removed it (the gui version which is pamac-gtk) and now i just type “yay” to my command line and i am loving it. Don’t need that GUI really. Install yay.
You can still use pamac and pacman from the command line.
It does cause issues.
Because pamac fails to make a distinction and proper preference.
It is not uncommon for users to end up with packages, including core packages like pamac-cli, replaced from the AUR so long as the package with the same name exists in the AUR.
(recently some of these have been mitigated simply by the AUR package getting a name change, like libpamac, but is still true for others like pamac-cli and pamac-tray-icon-plasma)
Its one of the reasons to not use use the AUR, not with pamac, not on Stable branch, not if you are not somewhat familiar with package management.
Yes, it can cause similar issues for users on stable branch when update announcements are delayed and AUR has a later version available
That is why experienced users suggest updating Repository packages before rebuilding AUR packages
Well I do need the GUI - if I want to search for something and have all versions across all repos/AUR/Flatpak listed.
So now I am glad to have noticed that I can have updates automatically download, I had missed the AUR dropdown ‘Check for updates’ applying only to AUR option.
So now running Pamac updates will do repos and flatpak (which YAY does not do).
If you want an ALL in one solution, try topgrade - and disable the 'self-update` option in the config, that’s more for ‘stable’ distributions.
I don’t use third party packages like flatpak, snap or appimage. I don’t think any sane person is happy to deal with more than one type of package in his/her setup. To be honest with you, i am new to Manjaro and arch itself. And i am finding out that there is manjaro’s own repos, arch repos, aur repos, and maybe even more, which is, and i think you agree with me here, just a nightmare. And when you say you also use flatpak or snap, that is also an addition to the already confusing package soup. But of course, if the package is there and nowhere else, you just have to i guess.
Thanks for the recommendation. I will check topgrade.
You might want to re-read whatever you have been looking at.
While all those things exist … by default Manjaro only uses its own Repos. Thats it.
Being contained bundles and cross-platform Flatpak and SNAP are also available if desired.
If you have some experience there is also the AUR.
You should not be using Arch repos on Manjaro - Manjaro repos are derived from Arch with some changes.
