via Terminal/Totalterminal or iTerm, this script works very well:
cd ~/go/to/dir/ && R -e "shiny::runApp("/go/to/dir", launch.browser=TRUE)"
but as/in a App via Automator, the second Part wont work.
In Automator: run Shell-Script. Where is the difference of "normal" Terminal and the Terminal used by Automator. In both /bin/bash