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About why works in Arduino IDE and not with XDK; in the IDE you are not using the mraa library, and with XDK you do, the error that you are having is related to this library or the code that you are trying to run.
First, you will need the latest mraa version in your board:
echo "src mraa-upm http://iotdk.intel.com/repos/1.1/intelgalactic" > /etc/opkg/mraa-upm.conf opkg update opkg install libmraa0
Could you attach the script that you are using, the "main.js"?
Thanks CMata, your answer clarified my questions.