Are you referring to the FTP "problem" where Win or Mac to Linux files throw in an extra char for newlines? In that case, ALL newlines are affected, not just the first line. I'm not sure whether Perl likes funky chars like ^M in it's parsing engine, so a sort of converter would be in order. All it needs to do is convert the DOS newline to the '\n' (that's the C character \n and not the Perl \n for your info, but under Linux the C code is \n anyway...) I'm sure there is already one readily available somewhere on this site....hmmm...

The second problem (seemingly unrelated) deals with a text file busy response. That's not a perl error response (at least not in <5.6 since I just looked it up in an old book) and probably has something to do with a mandatory lock failure on open(). I can't imagine that perl tries to lock the file (does it, though?), so you are probably using a linux kernel with mandatory locking compiled in...is that right? Anyway, I don't think emacs is locking the file (it does not, by default, unless...well, not by default). What made you cp it somewhere else and back. If this were mandatory locking, cp would fail on the open read just as perl would. No- something is fishy in your story. (p.s. emacs will not IN ANY FASHION insert a hidden character as you propose unless you save it in some strange manner (DOS mode?) and these two problems that you are having are unrelated!)

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