There are a couple of things I would try right off of the bat. First, I would suggest removing the following two lines from the autonomous and usercontrol functions, respectively:
These two function calls are simply placeholders in the template until user-defined code is put in; the AutonomousCodePlaceholderForTesting(); for instance will call to a function that has this code in it:
If this function is called first in autonomous before any other code is run, it will 'lock down' the robot in autonomous until autonomous ends. The UserControlCodePlaceholderForTesting(); function isn't as controlling, but it does have a 100 millisecond wait period in it:
I would suggest getting rid of these two lines first just to see, and if that doesn't work, double check that you have VEXNet connected properly, the Compiler Target is set to Physical Robot, and that the Cortex can communicate with the Joystick Controller; we have a full setup guide
on our wiki you may want to look at.
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