Well, first sorry to bump this post but since my problem came using the guide posted here, I think this is the best choice.
I've followed the guide on OSX tweaking all the differences between the original Windows config to mine, and I got Eclipse to successfully build the library and the Blink project. I also followed a tip from Zad to generate a .bin file although it didn't solve my problem.
The thing is that despite the file is compiled (I think) correctly, and flashed without errors to the DUE, it doesn't work. The .hex file is 126kb and the .bin is 45kb. Any idea what can be wrong or any way I can debug it?
Anyway, thank you Nassarane for the guide, it's the only one I've found around and it's pretty straight forward.
And now my two cents:
One of the differences I encountered between Windows and OSX was the external tools part. The first tweak to Nassa's code is to change the way arguments are passed to Bossac inside the script. The unix command is $@ in stead of %*.
Then, the main change is how to erase the flash memory. If you run $ stty -f /dev/tty.usbmodemxxx 1200 from terminal it works perfectly, but it doesn't work from a script. To make it work this way you have to tweak ".Profile" file and I didn't feel like changing system files. So I came up with another solution, using a very simple Python script. You need to install Pyserial library to get it to work.
So now I have two script files: arduinoDueFlash.sh in bash, and eraseDueFlash.py in python. Here's the code:
arduinoDueFlash.sh
#!/bin/sh
python /Path/to/eraseDueFlash.py
sleep 1
/Path/to/bossac $@
eraseDueFlash.py
import serial
s = serial.Serial(port='/dev/tty.usbmodemXXX', baudrate=1200)
s.close()
It may also work a solution like Nassa's using the very argument to set the port and not to hardcode it. I'll try it eventually.
You must also check the path in the arguments you put in Eclipse:
--port=tty.usbmodem411 -U false -e -w -v -b ${workspace_loc}${project_path}/Release/${project_name}.bin -R
This works for OSX, I guess it works as well on any linux but I don't know if there's a simpler solution to open the port.
Cheers