The warning is telling you that your filename contains a newline. That's because when you do my $filename =<STDIN>;, it's including the newline that's generated when you press Enter.
So when you see:
enter file name
And you do
myfile<ENTER>
$filename gets "myfile\n" as its contents. If you chomp() $filename, that will get rid of the newline in the variable, and as such the error. So you could do:
chomp( my $filename = <STDIN> )
to fix it.
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