I have been playing around with Rcmdr since I saw several folks talk say good things about it. To make it play nicely R-Portable I decided to create my own PortableApps icon to launch R-Portable and automatically start Rcmdr. The procedure is similar to creating a shortcut for Rcmdr except that I will start R-Portable from a separate folder that contains a customized version of .Rprofile that automatically starts Rcmdr. So I created a Rcmdr folder in my Portableapps program directory, created a DOS batch file that starts R-Portable with the “—sdi” option, and created a .Rprofile file like Scott Hyde had recommended. You can test your setup at this point. I am assuming you have previously installed R Commander. When you execute the batch file a DOS screen should briefly flash and both the R and the “sdi” version of the R Commander window should open.
To get a PortableApps icon to appear I created the PortableApps folder structure in Rcmdr, created an appinfo.ini file that referenced the batch file as the program executable, and copied the R icons from R-Portable into the “app\appinfo” folder. Now when I refresh my PortableApps icons I have a “R” icon for R Commander Portable to go with my existing icons for R Portable and RStudio Portable. Here is a zipped version of my Rcmdr folder,