In my opinion, Keras with back end tensorflow support and MXNet would be the best available R packages (for deep learning API compatible with R ) to deal with CNN.
Along side of CPU processing they both support faster GPU processing.
Here is one nice book " Deep Learning with R " written by " François Chollet with J. J. Allaire " which will be release on upcoming January 2018. I believe contents of this book would be enough to learn deep learning in R with Keras and Tensorflow implementation.