Unless your compiling and linking to build a monolithic, or static, executable, (all code included in one executable), it's shouldn't be much trouble. Most applications use dynamic linking of libraries at runtime, ie; .so files in linux. So, if you're making graphics function calls to GLES routines, usually via the Mesa lib, you just need to be sure there is a GLES compliant shared .so lib on both devices. You compile and link your code with the appropriate header files that contain the GLES function declarations and any macros needed."the trick is to make sure you don't accidentally link your code to a raspberry pi-specific library. As the only one that comes to mind is the GLES driver you'll probably be fine".
You can check the linux distro that you intend to have on the RK3066. Most mainline distros have repositories that list what applications and libraries ship with them. For instance, a Ubuntu repository: https://launchpad.net/ubuntu/+source/mesa As far as being on the device, you can try this on the command line: ldconfig -p | grep libgl2-mesa for instance. If the driver is there, you'll have output.
I don't believe that was the issue. The OP is compiling code on an RPi to install on another ARM device. The question arose about a potential issue concerning GLES compatibility and how to avoid it. Hardware is not the issue.
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