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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In reply to Re: How to see the processId of the process called by system command from perl by elmex
in thread How to see the processId of the process called by system command from perl by advait

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