Unable to Update Some AUR Packages

General system Pacman & AUR helpers
1

For about a month I’ve a problem updating micromamba through yay.
Within the last week it as now affected two more packages in the AUR for me and all refuse to update. Now cogl and clutter-gtk are affected.
I have tried installing all using yay or manually using git and makepkg.
All three seem to give the error of

ModuleNotFoundError: No module named ‘giscanner._giscanner’

I found some people having similar problems and suggested deactivating conda and trying to install, but I still run into the same issue.

I have also seen a suggestion in running the command g-ir-scanner by itself and should be seeing the error ERROR: Need at least one filename

However I also run into the aforementioned ModuleNotFoundError.

My guess is that perhaps my conda or python installation maybe at fault.
Python version installed 3.10.13

Conda version install 25.11.1

Perhaps of important note, I have ComfyUI installed on my system.

2

Welcome back @Zer0sVoid :waving_hand::smiley:

So if I follow, micromamba is having trouble compiling?

Have you tried using micromamba-bin instead? (pre-compiled)

3

Thanks for the welcome back!

Yeah, seems like micromamba and the other two packages have trouble compiling or updating.
I’ll try micromamba-bin and report back.

4

I ran into similar problems with pyenv. Can you open a fresh terminal, one without conda involved? What does python --version return on each? I’m betting that the system version will see the offending module.

In a nutshell, don’t run yay in a virtual environment.

5

Deactivating conda, opening a new terminal and running python3 --version returns Python 3.13.11

micromamba-bin seems to compile alright. When it checks for dependencies I’m seeing it would break a dependency.

removing micromamba breaks dependency ‘python-libmambapy’ required by python-conda-libmamba-solver

6

Hmm. micromamba lists that it provides libmamba, python-libmambapy.

micromamba-bin however specifies that it only provides micromamba.

python-conda-libmamba-solver has a dependency on python-libmambapy, which only micromamba is set as providing :downcast_face_with_sweat:

I don’t know enough about Mamba to be sure if you could simply edit the PKGBUILD of micromamba-bin and add that it provides python-libmambapy.

provides=(
   "${pkgname%-bin}"
   "libmamba=${pkgver}"
   "python-libmambapy=${pkgver}"
)
7

When did you upgrade last? I’ve been on 3.14 for at least a couple of weeks now. What does which python return?

8

That’s an excellent point @ajgringo619. Python 3.13.11 was superseded in the Arch repos by 3.14.2 (and more since) on Dec 14 2025 :grimacing:

9

I can’t recall the last time I updated python.
which python returns /home/USER/miniconda3/bin/python

10

Any time you install something, you should do so with an updated system. Partial updates will cause issues.

Using yay -Syu somepackage initiates an update at the same time as installing the package in question.

Given that it’s been perhaps 2 months since you updated, maybe focus on that first?

eos-update --yay
11

Ah, that’s a habit I have not formed. I’ll try to remember for the future. :sweat_smile:

I tried running eos-update --yay, but the same three packages still refuse to install and my python is still at the same version.

12

Ok, either try just:

eos-update

Or, if they’re AUR packages, use eos-update --yay but explicitly skip just those packages for now. Get your system up-to-date, reboot, then address those packages.

13

This is the problem, then. Try this:

  1. run /usr/bin/python, type import giscanner._giscanner, then enter

What is the result? I can’t stress enough how important it is to run system packages with the system python. All of the modules that these programs depend on are in directories that the system version of python is expecting.

14

Oh, my issue maybe my system python causing an issue.

Running your suggestions returns
Traceback (most recent call last):
File “”, line 1, in
import giscanner._giscanner
ModuleNotFoundError: No module named ‘giscanner’

15

OK, now try the exact same thing with the python that your previous which python returned.

As I mentioned above, I ran into issues like this when I had pyenv installed. I was constantly having to maneuver around what my terminal thought was the correct default python. I’ve since switched to uv, which is not only faster but a 100x easier to manage.

16

Doing the same thing with what my which python returned give me
Traceback (most recent call last):
File “”, line 1, in
import giscanner._giscanner
ModuleNotFoundError: No module named ‘giscanner’

You might be right about having multiple versions of python running.
I had some issues with ComfyUI a while back and that’s why I mentioned it in the original post.

17

At some point, though, you did install the micromamba package, correct? If so, the giscanner module has to exist somewhere. I would try searching the following directories listed in these python commands (run once for /usr/bin/python, once for the other):

python -c "import sys; [print(name) for name in sys.path]"
18

That’s right, micromamba is currently installed and refusing to update at the moment.

For usr/bin/python I get

/usr/bin
/home/USER/stable-diffusion-webui
/home/USER/miniconda3/lib/python313.zip
/home/USER/miniconda3/lib/python3.13
/home/USER/miniconda3/lib/python3.13/lib-dynload
/home/USER/miniconda3/lib/python3.13/site-packages

For the other
/home/USER
/home/USER/stable-diffusion-webui
/home/USER/miniconda3/lib/python313.zip
/home/USER/miniconda3/lib/python3.13
/home/USER/miniconda3/lib/python3.13/lib-dynload
/home/USER/miniconda3/lib/python3.13/site-packages

I might have been running into issues with python and stable diffusion webui instead of comfyui.
I don’t use stable diffusion anymore.

19

What happened to the 3.10.13 version you mentioned earlier? conda is definitely getting in the way. Here’s my (2) current installs:

/usr/bin/python

/usr/lib/python314.zip
/usr/lib/python3.14
/usr/lib/python3.14/lib-dynload
/usr/lib/python3.14/site-packages

/home/ajgringo619/.local/share/uv/python/cpython-3.14-linux-x86_64-gnu/bin/python3.14

/home/ajgringo619/.local/share/uv/python/cpython-3.14.3-linux-x86_64-gnu/lib/python314.zip
/home/ajgringo619/.local/share/uv/python/cpython-3.14.3-linux-x86_64-gnu/lib/python3.14
/home/ajgringo619/.local/share/uv/python/cpython-3.14.3-linux-x86_64-gnu/lib/python3.14/lib-dynload
/home/ajgringo619/.local/share/uv/python/cpython-3.14.3-linux-x86_64-gnu/lib/python3.14/site-packages

Yours are identical.

EDIT: well, at least I know now where you got Python 3.10 from: it’s a hard dependency of stable-diffusion-webui-git. This package is orphaned at the moment, with no updates since 2024.

20

That’s right, 3.10.13 seems to be from my stable diffusion install, I once I commented out the python path from my .bashrc I no longer see any 3.10.13 when I run python3 --version.

Perhaps deleting stable diffusion webui is a good idea.