Part2-Analysis issue

[fxm200013]

I am stuck in part2.

I get this error.

RRuntimeError: Error in (function (filename = "Rplot%03d.png", width = 480, height = 480, :
Graphics API version mismatch

I am running it on a cluster and I am using ipython to run it instead of python

These are my files

Seq2_trial1-networks-part2.txt
run_part2.txt

[melomcr]

It looks like you exported a jupyter notebook into a text file, which is already something that can cause issues with jupyter cell magics, but you kept the initialization of the rpy2 package and R modules without using them. Since your error is related to an R runtime and its graphical interface, I would suggest commenting out all cell magics executions related to 'R'.
That said, I have no idea why your script would be calling a graphics api.
You are also loading nglview and ipywidgets without using them, and both have graphics outputs, so maybe remove those as well.

If you do want to add R analysis and produce plots similar to the ones in the tutorial, I provided an alternative approach for using R analysis through a CLI (for remote execution in a cluster, like you are doing) in the CLI version of the tutorial Step 2. This does not rely on a graphical interface, but will still save plots to file for later analysis and publication.

The DyNetAn package version 2.0 introduced API changes, so make sure you are using the matching version of the tutorial. If your pipeline used DyNetAn version 1.2, make sure you get the tutorial version 1.2.