R - libraries...

One thing to note is that by default R will want somewhere to store any libraries you download.  Just as a matter of style I always try and detach libraries from the core.  The default on Windows is something along the lines of

C:\Program Files\R\R-3.1.1\library
C:\Program Files\RRO\R-3.1.2\library

I prefer to have my code and any supporting libraries on a different drive, so will create a folder called:
Where I will setwd() a new folder per project

I move the C:\...\library folder to D:\Users\myname\Code\R\library  and then create a symbolic link (junction) to fool the application into believing everything is in the right place: 
So from a command prompt I execute
C:\>mklink /J "C:\Program Files\R\R-3.1.1\library" "D:\Users\myname\Code\R\library"

The command prompt should return

Junction created for C:\Program Files\R\R-3.1.1\library <<===>> D:\Users\myname\Code\R\library

That's just me, no need to do that.