Hi I have an R script which invokes WriteXLS() (from the package of the same name) which as you may know, calls perl via system(). I've noticed that when I enable profiling using Rprof(), when the script gets to the part where perl is called, it gets "stuck": it just sits there using 99-100% CPU and around 10% of the RAM, and the perl command does not even show up as a running process under 'top'. While it is churning away, new profiling results continue to be written to the profiling file (at which point the entries are all "system" / "WriteXLS"). I have also noticed this behavior with other system() calls; not just perl. I've also tried pipe(cmd, open = "r") as an alternative to system(cmd) and the result is the same. I have tried in interactive as well as non-interactive mode, and the issue occurs in both modes although seems to be more common in the latter. So, I'm wondering if perhaps Rprof() + system() not a recommended combination ? I did notice from ?Rprof that "the profiler interrupts R asynchronously"; though I do not know what that means, perhaps that is somehow relevant? This is running on R version 3.2.1 under linux (RHEL6). Any suggestions would be greatly appreciated. Regards Ben