You haven't said enough detail about the nature of the libraries you want to call, but if your needs are simple enough, you could just write a main loop that reads JSON lines from stdin, calls a function by name, and writes a JSON line back to stdout. This works on all OSes and calling perl functions by package name is so simple you don't need a framework. If you need to manage persistent objects, you could extend it with a concept of a "stash", or even just eval lines of input as perl, or maybe a combination of the two so that you get the benefit of parsing JSON for the data exchange but can still tell it to eval some things. Maybe the first line of input is JSON and the second line of input is code to eval using the $data from the previous line? Lots of options here.

I've never used R, but I assume most languages have the ability to start a child process and read/write lines to it.