Interesting that R has a proto package, but to be honest, if I get to the point where I need classes or prototypal inheritance in R, I reach for another tool. R is excellent for exploratory data analysis, but in my (admittedly limited) experience with R, it makes for a poor choice for anything more complex than a small script.
For prototypal inheritance in R you can try the proto package [1].
[1]: http://cran.r-project.org/web/packages/proto/index.html