Using the last version available (1.4.2), calling overlapPermTest with verbose=TRUE, it throws the following error:

Error in random.evaluate[, i] : incorrect number of dimensions

I think there's somthing around line 157 of permTest.R, since this error happens at line 174 when verbose=TRUE. When verbose=FALSE everything is fine.

That's true, thanks for the heads up! I think when we updated the permTest function to deal with multiple evaluation functions we broke the code supporting the verbose output in (basically a progress bar) when performing the computations in parallel. We will fix this in the next version of regioneR, but as a workaround you can set verbose=FALSE or set force.parallel=FALSE if you really want to see the progress bar, although it will make the computation slower.