Warning messages keep appearing in RStudio notebooks in chunks unrelated to the warnings

You will see warning messages until you clear them out. Running warnings() function does not do that. To clear warnings you can execute the following command:

assign("last.warning", NULL, envir = baseenv())

The best approach though is to fix your code so the warnings are not produced. One way to deal with it is to use tryCatch() in R.

You can also disable all warnings by using supressWarnings() function, but this is not recommended since this will prevent you to see any of them.