It sounds like the immediate cause of the problem is unescaped regex metacharacters. You can fix that with quotemeta or /\Q$foo\E/ in the regex.

From your description of the problem, it sounds like the eq operator might do better than a regex.

Your algorithm seems to be quadratic. You would speed matters by taking each line, or an md5 digest of it, as a hash key. You would then only need to check existence of a key to find like lines.

Update: Here is an example:

my %filehash;
{
    open my $fh, '<', '/path/to/file_one.txt' or die $!;
    $filehash{$_}++ while <$fh>;
    close $fh or die $!;
}

{
    open my $fh, '<', '/path/to/file_two.txt' or die $!;
    while (<$fh>) {
        print qq("$_" is not in file one\n)
            if not exists $filehash{$_};
    }
}
[download]

Thank you very much for the quick responce.(By the way is there a way in this forum I can assign point or something like that).
I guess you're right about the quadratic algorithm if it can be called algorithm anyway. Where can I read more about your comment?Could you give me an example of code...
Thanks again.

(By the way is there a way in this forum I can assign point or something like that)

Voting/Experience System

--
edan

If you're using the lines of file 'A' as a regexp to match in file 'B', the problem you're experiencing is that most non-alpha characters have special meaning in regexps. What you need to do, if you require a regexp match based on the contents of file 'A', is to use quotemeta to prepare the search string so that its content won't be interpreted as regexp special characters.

Thanks a lot.It worked like miracle.Quick and great solution.
Thanks.