Is it possible to use the 'system' command for a raspberry pi in a compiled script?

I am having difficulty compiling some code using the Application Compiler. Currently, I use the 'system(rpi,...)' command to send commands to a connected raspberry pi. However, there seems to be a conflict, because the default Matlab 'system' command does not take objects, such as 'rpi', as a input to 'system'. So I get an error in the compiled program. Is there a workaround?

Thanks!