clusterCells functions crashes R

[JSDalcin]

I am having trouble with clustering my Giotto data, either with doLeidenCluster, doLouvainCluster or clusterCells. I have inputed the code proposed in tutorials for Visium datas and whenever i get to this part, R session abort. This problem happens on 2 different computers, with different versions of R (still above 4.1), different versions of Giotto Suite (3.2 and 3.0.1) and two objects, a bigger one and a smaller one.

gobject <- doLeidenCluster(gobject = gobject, resolution = 0.4, n_iterations = 1000)

For more context, I am running R version 4.1.1 (or 4.1.0) and Giotto version 3.2 (or 3.0.1).

[RubD]

Hi @JSDalcin, is this something that happened recently and does it happen with any of the example datasets/tutorials? Or only with your own data?

[JSDalcin]

Hi @RubD ,

I am new to Giotto so this started happening yesterday but it's the first time that I'm doing an analysis using Giotto. I was using Seurat until now. I did try it with my own data and tutorial data (Visium Mouse Brain), encountering the same problem.

[RubD]

Do you see this problem when you run the example tutorial starting from a fresh R/Rstudio start? Thus, without loading any other libraries. It's hard to figure out what's happening since I can't reproduce this on any of our hardware.

[RubD]

@JSDalcin I encountered a similar issue on a macOS (Catalina) machine and upgrading my R version to 4.2.3 has solved the issue for me.