Note kennethk's comments regarding the two parameter open in his reply to the OP!

What kennethk forgot to mention was that you should use lexical file handles too.

open ... $filename || die makes for an unhappy life. || binds to $filename, not to the result of open as you may be hoping. $filename is true for all likely values so the die will never fire, regardless of what the result of the open is! Use open ... $filename or die instead. It's often helpful in the die to show the error message associated with the open failure using $OS_ERROR ($!).

Making those changes, removing extraneous () and minor adjusting of white space produces the following (untested) code:

#!/usr/bin/perl
use strict;
use warnings;

die "Usage fileReference File2Check >outfile" if @ARGV != 2;

my ($fileRef, $file2Check) = @ARGV;

open my $fileREFIn, '<', $fileRef or die "unable to open $fileRef: $!"
+;
open my $fileCHKIn, '<', $file2Check or die "unable to open $file2Chec
+k: $!";

my %seen = map { chomp; $_ => 1 } <$fileREFIn>;

print grep {! $seen{(split /,/, $_)[0]}} <$fileCHKIn>;

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True laziness is hard work

In reply to Re^2: list lines not found in config (while+if) by GrandFather
in thread list lines not found in config (while+if) by tangledupinperl

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