"reached elapsed time limit" warnings RStudio

Thanks for your help andresrcs. Unfortunately none of those suggestions fixed my problem, but I think I figured out how to fix it. I noticed that when I open a script and run it the first time there are no warning messages. It's only when I rerun the script that I get the elapsed time reached messages. I tried adding the line gc() to free up memory from the previous run and I stopped getting the warning messages altogether.

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