How are you calling the R script? With the system function? Are you forking before you call it? Is the script going to the background? Best way would probably be to fork and call the R script in that new process via system:

my $pid = fork;
defined $pid or die "fork failed: $!";

if ($pid) { # in parent:
   waitpid $pid; # wait for the child, which's pid is in $pid

} else { # in child:
   system ("R ...");
   exit;
}
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