There is a similar question on the Arduino forum but I don't know if your issue is exactly the same: [FIXED][CapacitiveSensor] Can't compile with Due (port manipulation)
It doesn't look like the Arduino folks are very responsive. The user modified register names and eventually put his own library out there.
*"...changed the uint8_t registers to RwReg (compiler doesn't complain) and I replaced the use of portModeRegister(PIN) with simple pinMode(PIN, MODE) calls (it's slower but it works)."*