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Files created on Windows have different line-endings from the ones used on Unix. Transferring files between systems (even program files) leads to strange results. After you transfer a file from DOS to Unix, be sure to say 
dos2unix dosfilename unixfilename
The DOS line ending will often appear as M in files opened in Emacs. If you see that you will know what to do.
Andre de Souza
2012-11-19