CR characters are in site-gentoo.el because 50ruby-mode-gentoo.el has CRLF's for new lines. Other packages provide such files with unix style line breaks. Reproducible: Always Steps to Reproduce: 1. emerge app-emacs/ruby-mode Expected Results: No CR characters should be in site-gentoo.el. Please use only LF for each new line.
Thanks for the note. Fixed in CVS.