Prolog – Arguments are not sufficiently instantiated

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I am writing this answer, because the best answer yet was in a comment by lurker. I want to have it show up as an actual answer.

Your code is not working, because you’re doing R1 is R+1 when R isn’t instantiated in the case not_number([X|T], R). Your recursive case is strung a little backwards. You want to do this:

not_number([X|T],R):- 
    not(number(X)),
    not_number(T,R1),
    R is R1+1.

Now the right side of the is is instantiated when it is called.

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