For using the serial line of the Raspberry Pi you have to make some small modifications (just if you hadn't run the alamode setup):
In the file: /boot/cmdline.txt
change:
dwc_otg.lpm_enable=0 console=ttyAMA0,11520 kgdboc=ttyAMA0,115200 console=tty1 root=/dev/mmcblk0p2 rootfstype=ext4 rootwait
to:
dwc_otg.lpm_enable=0 console=tty1 root=/dev/mmcblk0p2 rootfstype=ext4 elevator=deadline rootwait
And in the file: /etc/inittab
comment out:
2:23:respawn:/sbin/getty -L ttyAMA0 115200 vt100
to:
#2:23:respawn:/sbin/getty -L ttyAMA0 115200 vt100
Because the Arduino IDE is not able to find the tty connection of the serial port (ttyAMA0) you have to mirror it to ttyS0. That is to be done with a file in: /etc/udev/rules.d
then name it (the number is according to the order in which the rules were loaded):
85-paperduinopi.rules
and put in the following line:
KERNEL=="ttyAMA0", SYMLINK+="ttyS0",GROUP="dialout",MODE:=0666
More informations:
www.andremiller.net