Weird package/mirror confusion with my setup

[tt_tez]

Hi, I’m new on CachyOs and Linux. few weeks ago I learned that there is a tool called topgrade and it upgrades system much better su by using it I think I changed my mirrorlist and used/upgraded the system like that for a while…

Then one day I have noticed that I am not on the correct repo and reverted to CachyOs v3 mirrors for my cpu.. then the problems started to arise I don’t have cached old package versions and also I do not have a snapshot state before using topgrade… What do you guys think is the best approach would be here? I don’t want a messy system that I always ignore some packages..

here is the topgrade command part that I messed up probably (merged mirrors or overwritten them)

── 00:31:05 - Configuration update ─────────────────────────────────────────────
==> pacnew file found for /etc/pacman.d/mirrorlist
:: (V)iew, (M)erge, (S)kip, (R)emove pacnew, (O)verwrite with pacnew, (Q)uit: [v/m/s/r/o/q]

and here’s the current situation. I tried removing spectacle and reinstalling it but it cannot reinstall it so I reverted back with snapshots

❯ sudo pacman -Syyu
[sudo] password for ozu:
:: Synchronising package databases...
 cachyos-v3                      122.2 KiB   745 KiB/s 00:00 [################################] 100%
 cachyos-core-v3                 114.9 KiB   684 KiB/s 00:00 [################################] 100%
 cachyos-extra-v3                  4.3 MiB  6.24 MiB/s 00:01 [################################] 100%
:: Starting full system upgrade...
warning: bash: local (5.3.15-1) is newer than cachyos-v3 (5.3.9-2)
warning: ripgrep: local (15.1.0-3) is newer than cachyos-v3 (15.1.0-2)
warning: zstd: local (1.5.7-3) is newer than cachyos-v3 (1.5.7-2)
resolving dependencies...
warning: cannot resolve "qtkeychain-qt6", a dependency of "plasma-nm"
warning: cannot resolve "tessdata", a dependency of "tesseract"
warning: cannot resolve "tesseract-data-osd", a dependency of "tesseract"
warning: cannot resolve "tesseract", a dependency of "spectacle"
:: The following packages cannot be upgraded due to unresolvable dependencies:
      plasma-nm  spectacle

:: Do you want to skip the above packages for this upgrade? [y/N] y
looking for conflicting packages...
 there is nothing to do

~ 9s

[cscs]

Hello and welcome,

@tt_tez

here is the topgrade command part that I messed up probably (merged mirrors or overwritten them)

── 00:31:05 - Configuration update ─────────────────────────────────────────────
==> pacnew file found for /etc/pacman.d/mirrorlist

So does that mean you overwrote with the pacnew your mirrorlist file is fully commented out?

You could share it with something like;

paste-cachyos /etc/pacman.d/mirrorlist

But it seems like a copy of the same scenario as this other thread;

Cant install clamav

As foretold.. You could also run some sort of mirror sort utility. In the case of the Arch mirror file you can even shape and download it from the website;

So you can follow the advice there to get a working mirrorlist again.

But also follow the links to get more informed about how to properly handle pacnew files;

Questions about managing Pacnews

The cases in which you should either replace or remove one or the other are few. In the vast majority of situations they should be manually reviewed and merged as needed. That is using the v (view) option of pacdiff to show the comparison and make edits by hand. ( While a m (merge) option exists it should not be blindly trusted to make these kinds of decisions/edits/operations. ) For example locale.gen.pacnew might have some new locales added to the file. So you would merge those new lines …

[tt_tez]

Here iss my mirrorlist now. But I think now it is correct but I messed it up before and upgraded system with that config. Now mirrors are correct but packages are not probably some of them are from v4 repos and they can not update now.. I had no idea about pacnew files I will research it now thank you!

mirror list

[cscs]

@tt_tez

But I think now it is correct

Seems it is .. or at least there are enabled mirrors there.

@tt_tez

Now mirrors are correct but packages are not

What is the output of

sudo pacman -Syu

[tt_tez]

:: Synchronising package databases...
 cachyos-v3 is up to date
 cachyos-core-v3 is up to date
 cachyos-extra-v3 is up to date
:: Starting full system upgrade...
warning: bash: local (5.3.15-1) is newer than cachyos-v3 (5.3.9-2)
warning: ripgrep: local (15.1.0-3) is newer than cachyos-v3 (15.1.0-2)
warning: zstd: local (1.5.7-3) is newer than cachyos-v3 (1.5.7-2)
resolving dependencies...
warning: cannot resolve "qtkeychain-qt6", a dependency of "plasma-nm"
warning: cannot resolve "tessdata", a dependency of "tesseract"
warning: cannot resolve "tesseract-data-osd", a dependency of "tesseract"
warning: cannot resolve "tesseract", a dependency of "spectacle"
:: The following packages cannot be upgraded due to unresolvable dependencies:
      plasma-nm  spectacle

:: Do you want to skip the above packages for this upgrade? [y/N]

I have those warnings that the current package is newer and I can not upgrade those 2 packages

[cscs]

Your system is still not correctly configured.

It is lacking all of the Arch repositories - it was originally guessed this was because of the missing mirrors but it seems the repos are simply not enabled in the pacman configuration file.

Did you ‘handle’ more pacnews than just the mirrorlist?

Or recently otherwise touch or configure /etc/pacman.conf?

Let us see that file;

paste-cachyos /etc/pacman.conf

[tt_tez]

pacman.conf

I might have handled more than one pacnews. I am not sure. and I updated pacman.conf with the current one assuming this is correct. How can I revert the original mirror list ? I can always go back to first snapshot but I want to avoid that since I will lose many things, not just files but also apps and configs of them…

[cscs]

@tt_tez

I am not sure. and I updated pacman.conf with the current one assuming this is correct.

As explained in one of the linked threads on pacnews .. it is rather rare that any pacnew file should either be blindly discarded or blindly used to overwrite the current file. In almost all cases the file should be manually inspected and compared and manually merged as needed.
That is using the v response to pacdiff -s.
( Or DIFFPROG=meld pacdiff -s or using some other comparison tool as needed. )
Then manually applying needed changes before deleting the pacnew.

@tt_tez

pacman.conf

As suspected .. the Arch repos are missing and we need those.

The bottom of the file should look more like this;

# cachyos repos

[cachyos-v3]
Include = /etc/pacman.d/cachyos-v3-mirrorlist

[cachyos-core-v3]
Include = /etc/pacman.d/cachyos-v3-mirrorlist

[cachyos-extra-v3]
Include = /etc/pacman.d/cachyos-v3-mirrorlist

[cachyos]
Include = /etc/pacman.d/cachyos-mirrorlist

#[core-testing]
#Include = /etc/pacman.d/mirrorlist

# arch repos

[core]
Include = /etc/pacman.d/mirrorlist

#[extra-testing]
#Include = /etc/pacman.d/mirrorlist

[extra]
Include = /etc/pacman.d/mirrorlist

# If you want to run 32 bit applications on your x86_64 system,
# enable the multilib repositories as required here.

#[multilib-testing]
#Include = /etc/pacman.d/mirrorlist

[multilib]
Include = /etc/pacman.d/mirrorlist


# An example of a custom package repository.  See the pacman manpage for
# tips on creating your own repositories.
#[custom]
#SigLevel = Optional TrustAll
#Server = file:///home/custompkgs

..following the existing example of no sigs.
My file actually uses SigLevel = PackageRequired on each, ex;

[extra]
SigLevel = PackageRequired
Include = /etc/pacman.d/mirrorlist

but yours does not so I did not include any such lines.

When you have made the requisite changes then please run a full sync/refresh/upgrade again and share the output;

sudo pacman -Syu

[tt_tez]

I also added SigLevel = PackageRequired to each of them just to add more security. After that it upgraded all the packages correctly thank you! here is the output;

:: Synchronising package databases…
cachyos-v3                      122.2 KiB   837 KiB/s 00:00 [################################] 100%
cachyos-core-v3                 114.9 KiB   751 KiB/s 00:00 [################################] 100%
cachyos-extra-v3                  4.3 MiB  6.37 MiB/s 00:01 [################################] 100%
cachyos                         513.8 KiB  1954 KiB/s 00:00 [################################] 100%
core is up to date
extra is up to date
multilib is up to date
:: Starting full system upgrade…
warning: bash: local (5.3.15-1) is newer than cachyos-v3 (5.3.9-2)
warning: mkinitcpio: local (41-4) is newer than cachyos (41-2)
warning: oh-my-zsh-git: local (r7801.5181447da-1) is newer than cachyos (r7425.7ed475cb5-1)
warning: proton-cachyos-slr: local (1:11.0.20260602-3) is newer than cachyos (1:11.0.20260601-1)
warning: rate-mirrors: local (0.29.0-1) is newer than cachyos (0.28.3-2)
warning: ripgrep: local (15.1.0-3) is newer than cachyos-v3 (15.1.0-2)
warning: zen-browser-bin: local (1.21.3b-1) is newer than cachyos (1.21.1b-1)
warning: zsh-theme-powerlevel10k: local (1:1.20.17-1) is newer than cachyos (1:1.20.15-1)
warning: zstd: local (1.5.7-3) is newer than cachyos-v3 (1.5.7-2)
there is nothing to do

~

I assume these warning will fade away by time/upgrades

[cscs]

It seems like some of those may have been upgraded from the AUR or some other source, possibly during the previous misconfiguration, but we should be able to at least get rid of those warning by including an extra u. Heck lets add the extra y too just because they were reconfigured;

sudo pacman -Syyuu

(The extra u allows apparent downgrades so should sync with the repos even if it looks like it would be a lesser version.)
(The extra y forces refresh of the databases - you will notice during this run all of the repos loading on the right even when previously only the ones needing changes did.)

[tt_tez]

Thank you I don’t know how I did this mess-up but you helped me understand what was wrong and how to deal with it ! Now there are no warnings and every package is up to date within correct repos !

[HardCode4All]

Reading this thread reminds me that I will never use anything else than pacman -Syu or cachy-update to update my system.

Whatever anyone says about tools like topgrade or pamac, threads like this one are proof enough for me that nothing beats the originals.

[cscs]

To be fair to topgrade, I believe it just called pacdiff so not really to blame I do not think.