...
$R->startR;
open FH, ">", "c:/scripts/test2.txt" or die $!;
...

##</code><code>##

#!/usr/bin/perl
use warnings;
use strict;
use Cwd;
use Statistics::R;

my $currentdir = cwd();
my $R = Statistics::R->new();
open FH, ">", "test1.txt" or die $!;

$R->startR;
$R->stopR;

chdir($currentdir);
open FH, ">", "test2.txt" or die $!;