In the "eigengen" function help we have:

(...)

If a non-null second argument is given, the specified matrix will be over-written with the auxiliary result. (It is not required that the existing matrix be of the right dimensions to receive the result.) It will be organized as follows:

(...)

When you say "It will be organized as follows", are you talking about the matrix that the function will output (A) or the existing matrix (U)?