Retina Macbook Pro 13" makes clicking noise once a second
The only moveable part in a retina macbook pro 13" is the fan as seen on the following picture: (courtesy of ifixit)



Therefore it must be an issue with the fan, particularly because the noise originates from the right side (imagine the macbook pro flipped and the fan will be on the right side). Either the fan failed or something got stuck in the fan and is preventing it from spinning. I suggest you take it into an Apple Store so they can have a look at it in detail.