lmHeatmap: node stack overflow

[f6v]

I'm trying to run the example with the simulated data, and I've got a failure on the following line:

lmHeatmap(scAI_outs, color.by = "labels")

Error in is.leaf(dend) : node stack overflow
Error during wrapup: node stack overflow
Error: no more error handlers available (recursive errors?); invoking 'abort' restart

Quick search led me to trying the following: options(expression = 1000000), though the result was the same. Have you seen this issue before?

I'm running R 4.0.2 on macOS.

Thanks in advance!

[sqjin]

Hi @f6v , I am sorry that I have not encounter such issue before. I have not upgraded my R version to 4.0. There might be some conflicts with R version or the ComplexHeatmap package.

[f6v]

Thanks, I guess the issue arises from jokergoo/ComplexHeatmap#539

[jokergoo]

Yes, that was a bug in ComplexHeatmap and a little difficult to fix. Can you add tiny noise to the matrix e.g.

scAI_outs = scAI_outs + runif(length(scAI_outs), min = -0.5, max = 0.5)*1e-5

[sqjin]

Thanks @jokergoo !! I just added a tiny noise to the matrix @f6v

[jokergoo]

Hi, I think I have fixed this bug. The problem was when there are too many identical rows or columns, the dendrogram will be very deep, which causes the recursive function which was used in ComplexHeatmap to generate too many stack calls. Now I have changed the recursive implementation with iterations and I think there should be no such error any more.

You can just update the version from Github if you want to use it now. I will do more testing and then I will push to bioconductor in the next few days.