Hi, some remarks:
- use "use strict"
- initialize your data before using it ($l is not initialized)
- you don't need rows, row1, row2 as temporary variables

The following script checks for an empty line with the
mighty regexp /^[\s]+$/ instead of
comparing with "".

#!/usr/local/bin/perl -w

use strict;

my (@names, @versions,$l,$e);

$l=0;
$e=0;
while (<DATA>) {
  chomp;
  if (! /^[\s]+$/) {
    ($names[$l],$versions[$l])=split(/[\s]+/);  
    $l++;
  }
  else {
    $e++;
  }
}

$,=", ";
print "@names @versions\n";
print "empty lines=$e\n";

__DATA__

jan 2.76
feb 3.20

mar 1.6
apr 4.00
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