Hey, I dug into the Adafruit library for the DS1307 and I have updated it to be compatible with the Arduino Due. I have attached a zip with the new Library in it. Be aware that the examples will apparently not work until you save them in the new ino file format. So open the example you want to run, resave it under a different name, and then it should compile and run. Also, are you planning on using the Adafruit breakout board for the DS1307?
Cheers!
RTClib.zip (5.54 KB)