I don't think print is the appropriate debugging tool here...

$ hexdump -C foo.txt 
00000000  46 6f 6f 0d 42 61 72 0d  51 75 7a 0d              |Foo.Bar.Q
+uz.|
0000000c

$ cat read.pl 
#!/usr/bin/env perl
use warnings;
use strict;
use Data::Dumper;
$Data::Dumper::Useqq=1;

open my $fh, '<', 'foo.txt' or die $!;
print Dumper([PerlIO::get_layers($fh)]) unless $] lt '5.008';
while (<$fh>) {
    print Dumper($_);
}
close $fh;
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Output on Win 7 Strawberry Perl 5.10, 5.14, 5.20, and 5.26:

$VAR1 = [
          "unix",
          "crlf"
        ];
$VAR1 = "Foo\rBar\rQuz\r";
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And on Linux, the output is as follows:

# 5.6.2:
$VAR1 = "Foo\rBar\rQuz\r";

# 5.8.1 and 5.8.9:
$VAR1 = [
          "stdio"
        ];
$VAR1 = "Foo\rBar\rQuz\r";

# 5.10.1 thru 5.26:
$VAR1 = [
          "unix",
          "perlio"
        ];
$VAR1 = "Foo\rBar\rQuz\r";
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So none of the tested versions handle a CR line ending. See also open: the default layers are :raw on Unix and :crlf on Windows. For details see also PerlIO and open (the pragma). (Update: and LanX provided another excellent link with Newlines in perlport)

If the file is plain ASCII, this works across all of the above configurations:

use warnings;
use strict;

open my $fh, '<', 'foo.txt' or die $!;
binmode $fh;
$/="\x0D";
while (<$fh>) {
    chomp;
    ...
}
close $fh;
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