I've used Rscript with the --vanilla flag successfully from the OS X command line in the past. To use in MATLAB, this is what I'd consider doing.
1. Prepend the following to the top of myscript.R, the program you want to run:
2. From the OS X shell, set the executable bit on your program if it hasn't been done:
$ chmod u+x myscript.R
3. Now, you're set up to use the system function in MATLAB:
The usual caveats about paths apply.
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