Also can you tell me what is wrong with this line of code
awayFromTheNumberArray = JellyBeansHelper.findLowestDifference(playerGuess, jeallyBeans);
I'd need to see the source, but you get an NPE when you're dereferencing (usually calling a method) on something that's null. So:
String s = null;
...would throw an NPE.
In terms of getting a string from the console, I presume you know how to do that already since it's being done in the above output? To convert that string to an integer and therefore store it in an int variable, use Integer.parseInt(string).
As for the array, it's really the wrong structure to use here, have you used arraylists? They grow dynamically so can store any number of values the user inputs, without you specifying the number first. You'd use a while loop, check for some character being inputted that marked the end of the user input for that array (such as "." or an empty string) and then in the while loop, read from the console and add it to the arraylist.