'Strange behaviour of Rmarkdown. It stops during execution for no apparent reason

I have recently run into a very strange issue with Rmarkdown. When I run a chunk that takes a few minutes Rmarkdown just stops at some point. This does not happen every time, but often enough. The chunk runs some Rcpp code. I can't produce an example because the routines run are quite lengthy, sorry. I am attaching a screenshot that shows the progress of the chunk, but also shows that Rmarkdown has stopped (no red button). When it stops it also does not redraw the viewer. enter image description here

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