twimaster.cpp for I2C (to get a MLX90614 to work)

Easy enough. The library appears to be written for the AVR Arduinos, accessing ports directly rather than making library calls. That code will not work with the Due as it is a different architecture. You'll need to figure out what that code is trying to do and recode it.

This is common in many libraries as people took shortcuts to get more horsepower out of the smaller units. It makes getting the hardware working on Due a painful process.