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That's correct. As a work around, chose an int value to represent the "?".

For example:
final static int QuestionMark = 54321; // this value represents a "?"

theArray[i] = QuestionMark; // ...

As Greg said: All elements of an array must be of the same type.

Why do you want a value in an int array to be a "?"?

You could chose one of the possible int values to represent a "?" and use...

The code in post#1 works for me. Are there any lines in source.txt?

It should be false after the lines are read.
Have you tried debugging the code by adding a call to println() inside the loop to print out the value of line each time it is assigned a value?