Laurent's changes 

Changes include
- DESCRIPTION dependencies and NAMESPACE to remove warnings and added MSnbase
- using message instead of print/cat; see http://bioconductor.org/developers/package-guidelines/#messages
- updated/added MSnbase section at the end
- other minor typos/fixes

I still see quite a few warnings due to codoc mismatches and missing docs. Let me know if you need any help with these.

Best wishes,

Laurent