The statement tries to stack a 2x2 on top of a (2x4) x 2
M = [diag(checkpoint)-diag(checkpoint); -eye(2) zeros(2); zeros(2) eye(2)];
x x
x x
x x x x
x x x x
x x x x
x x x x
for it to work the top 2x2 matrix would need to be padded to 2x4
Looking at it diag(checkpoint)-diag(checkpoint) doesn't make much sense - you'd just do zeros(2) in your schema. Maybe you meant to horizontally concatenate diag(checkpoint) with the unary negation of diag(checkpoint)
M = [diag(checkpoint) -diag(checkpoint); -eye(2) zeros(2); zeros(2) eye(2)];
