Passes R CMD CHECK

The package now passes R CMD CHECK with 1 warning and 2 notes
the warning is because some font problems in tex and the notes are because of ggplot plotting

I fixed all usage statements for methods, and all superflous function parameters.
All examples now work - there is a shitty feature that you have to put library() in each example segment if you're using GRanges. So each example that uses GRanges contains library(Genomic ranges)

The rest of the stuff is purely cosmetical

live long and prosper