Giotto Error: py_run_file_impl(file, local, convert) : ModuleNotFoundError: No module named 'dataclasses'

Question

[Agatha Nabilla L]

Hi,

I am trying to do Leiden Clustering, but it seems like the code doesn't work really well on my M1 MacBook Air.

Here the code I have run:

my_giotto_object_n = doLeidenCluster(gobject = my_giotto_object_n, name = "leiden_clus")

and here is the error message I got:

Error in py_run_file_impl(file, local, convert) : ModuleNotFoundError: No module named 'dataclasses'

I wonder what is wrong and please suggest what should I do to overcome this error. Thanks!

Answer 1

[Giacomo Rocchetti]

Looks like the function requires the module dataclasses as a dependency.
Try installing the missing dependency:

pip install dataclasses

and see if that solves your problem.

[Agatha Nabilla L]

Thank you for your suggestion, have installed it and use a specified python_path to execute the command, yet get this error message:

[Giacomo Rocchetti]

Seems like an error due to an installation of the wrong library (it does not match your machine's architecture). Try to clean your current installation and re-install the package with a manual installation (see the instructions here).

Hope this helps.

[Agatha Nabilla L]

Hi,

Thank you for your suggestion, I have created different virtual environment and after running it on R, I just realised that I use R version for intel-based Mac (x86_64-apple-darwin Bird Hippie) instead of the M1, then I changed to the R M1 (aarch64-apple-darwin20 Vigorous Calisthenics), yet upon installing the package, it gives me this error:

ERROR: dependency ‘lfa’ is not available for package ‘Giotto’

• removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Giotto’

Do you have any suggestion for this issue? thank you

[Agatha Nabilla L]

I finally created virtual environment for x84 for the python, so it matches with the R version and it works. Thank you for your help :D