Need guidance about update and problems after. (picom, polkit, replace kernel?)

Support System Updates
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Hello, I am more a ‘simple’ user of manjaro (in mabox version) and have no deep knowledge in the core system. My hardware is AMD Ryzen 5 5600G with Radeon Graphics.
After last update in december I urgently needed to run one now which provided a lot of challenges.

  1. Method of updating? I used the graphical interface (pamac), it started normal but in the middle of downloading the gui disappeared and I could not see the progress althrough the process seemed to continue.
    I did read that it is no longer recommended to use pamac and do the update with command line, right? Do you recommend yay -Syu ?
  2. I quickly ran out of disk space in my 32 GB partition, which was large at beginning, but after every update the system gets a lot bigger. There is no check of the update process to calculate required disk space upfront. Why?
    Can I use another partition of my disc as a temporary space? Or split the update in parts?
    Is there any log I can look into to see why after update now I need 1.4GB more space? ( After sudo pacman -Scc )
  3. After I managed to have enough disk space manually, the update did run through. So far I stumbled over the following issues:
    a) graphics problem with windows not updating. I remembered that this was also an issue last time and my picom setting was xrender, now I need to disable picom compositor with Super+P
    What is the configuration for this AMD Ryzen graphics? I hope I am not the only one out with this.
    b) I use kernel 6.1.176-1-MANJARO x86_64. This is now called an old kernel. What is the recommendation for an update for my system? Is it risky to try a new one? I had issues once with NTFS support, that the included driver made my files corrupt. I disabled this (blacklist ntfs3).
    Now with 6.1 I ran into polkit issues. The only thing that worked was to do
    sudo systemctl mask polkit-agent-helper.socket
    No idea what is behind this, but now I get the password prompt when running gparted or other system tools. Do I need to do something else? Do I have a big security risk?
    Flameshot was not working too, but I could solve this with the useX11LegacyScreenshot=true entry in the config file.
    What else should I look at ? Is there a better sorted database (maybe even AI bot) to find known problems ?
    Sorry for any stupid questions!
Guidance on Orphan / Alien (AUR)
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Hello @DataXL and welcome to the Manjaro Community! :vulcan_salute:

For system upgrades, I always recommend sudo pacman -Syu followed with your choice of AUR helper (in your case, yay) for the AUR packages.

For the Kernel, you can install others alongside it and choose which one to boot with from the GRUB menu. I’d recommend at least having the latest LTS (linux618) and it’s worth noting that there are issues with polkit with Kernels prior to linux612.

As for the NTFS issue: The new kernels won’t corrupt an NTFS filesystem; it’s quite capable of doing this all by itself. :wink: The difference is that the newer (kernel) drivers pick up on filesystem errors (e.g. “dirty” bit set) and refuse to mount RW to protect the contents from further damage.

By the way, I increased my / partition from 50G to 75G some time back. Things do tend to accumulate. Have you tried checking/clearing the logs? Those can get quite large if untended.

From what you posted, it appears you manually cleared the pacman cache?

Also note: Not stupid questions! :wink:

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Welcome to the forum! :vulcan_salute:

Absolutely not. yay is an AUR helper, and it is strongly advised to not use any AUR helpers for updating your system packages, due to the possibility that they will pull in an AUR package with the same title as a repository package when both exist at the same time.

Update your system with pacman instead, and you can update the AUR packages afterwards — I use the command-line version of pamac for that. Also, always refresh your mirrors before running a major update. :backhand_index_pointing_down:

sudo pacman-mirrors -f && sudo pacman -Syu && pamac update --aur --devel

Recommended reading… :backhand_index_pointing_down:

If you use btrfs with snapshots, then you may need to delete some of the older snapshots.

There is if you use pacman.

If you have an empty partition with a Linux-native filesystem, then you can mount this volume to /var/cache/pacman/pkg before updating, and then this will be where your downloaded packages will be stored. You could even make this permanent by adding the empty partition to /etc/fstab with /var/cache/pacman/pkg as the mountpoint.

Some recommended literature to help you on your way… :backhand_index_pointing_down:

No, but — again — if you are on btrfs, then it may pay to check the usage of your filesystem, and if necessary, run a balance operation. :backhand_index_pointing_down:

It is advisable to completely log out of the graphical environment and log into a tty for updating the system — see my HowTo higher up this post.

AMD graphics commonly don’t require any additional configuration. They should work out-of-the-box, because the driver is in the kernel.

The recommended kernel is 6.18, which is an LTS kernel — it will be supported until (at least) December 2028.

Not if you stick to LTS kernels.

That is a very bad strategy. I would advise you to unmask it again and use a newer kernel.

The other solution, if you were to want to stick to 6.1, would be to set the SUID bit on /usr/lib/polkit-1/polkit-agent-helper-1.

sudo chmod 4755 /usr/lib/polkit-1/polkit-agent-helper-1

Note that this is only needed if you stick with the older kernel. On newer kernels it is advised to not have the SUID bit set on that file, because doing so is a security risk. That’s why the change was implemented in the first place.

See my reply here-above. :wink:

The forum has a built-in search function, albeit that — admittedly — it’s not exactly a good one. :face_with_diagonal_mouth:

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Thanks for such a lot of input. The SUID bit did not change the polkit problem, this is also reported here in the forum.

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Well, your best bet is still to upgrade to 6.18.

Do however note that you won’t be able to remove the 6.1 kernel while you’re still booted up into it So you’ll have to install 6.18 first, reboot into 6.18, and then remove 6.1.

And of course, you’ll have to remove the SUID bit again. :backhand_index_pointing_down:

sudo chmod 755 /usr/lib/polkit-1/polkit-agent-helper-1
2 Likes
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Also, if you have not updated several months, it is vital that you read the second posts of the announcements topics. I have trimmed the latest to about february, so if you need older go to some of the previous ones. The march one goes to mid 2025

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The developer of mabox is doing a great job and is indeed using Manjaro as the foundation.

mabox is providing a great UI for a keyboard oriented user.

I do think that you should try asking in the mabox linux forum as I am confident they know a lot more about the inner workings and how to solve issues for your system.

system maintenance

I am a huge fan of proper system maintenance because

  • The system does not maintain itself.
  • Obsolete packages does not remove themselves.
  • The package cache does not empty itself.
  • The kernel should not change major version itself.
  • Yet the kernel does change itself if it marked EOL (linux-meta magically appear)
  • The kernel packages continues to build up

Some ideas on how to keep your system in shape

[INFO] Stable branch - BIG update BEST practice

packages

If the Manjaro Package Manager pamac is installed on your system - you can set the number of packages to keep in the applications Preferences.

You can also use the Installed tab to find all installed packages, remove applications you don’t actually use. Especially note the Orphans and Foreign in the left pane of the Installed tab

All packages on your system contribute to the size of any update.

Always recheck your Orphans after removing an application, keep clicking remove all until the list is empty.

kernels

As you already know kernels older than 6.6 has issues with polkit.

You can use the Manjaro Settings Manager to weed out in your installed kernels.

My personal unofficial recommendation is to use the latest LTS kernel, which - as of 2026-07-06T22:00:00Z is Linux 6.18.

My personal experience is, it is rarely the kernel that prevents a system from launching the GUI, in most cases it is caused by the GPU driver, predominantly Nvidia.

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10 posts were split to a new topic: Veracrypt does not recognize ntfs3

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Super helpful thread, I feel like I’m kind of on the same mission as OP
This step ladder approach can help me get back up to speed from my 25.0.7 version I’m currently on. clearly the monthly consolidated updates mentioned need to be accounted for a long the way. Pamac being the key to all of this approach

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Updates: - I am now on Kernal 6.18, I discovered that I never choose 6.1. I was happy with 5.15, but since end of life I was put to 6.1 ‘automatic’. And this 6.1 Kernel has problems with picom AMD Ryzen and polkit, so not the best automatic choice.

  • My Veracrypt ntfs3 error could be solved by one line:
    sudo ln -s /usr/bin/mount.ntfs-3g /usr/bin/mount.ntfs3
    With that I could use the GUI, but maybe using cryptsetup is better.
2 Likes
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As part of this guide, I was also stand up my Manjaro back to 26.10 safely and am utilizing the 6.18 Kernel :+1:

Now I just have to safely navigate re-adding & updating my AUR’s per guidance above

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