Thanks @clairblacketer for considering us poor R users 
The develop versions of many of our packages now support 64-bit integers, including DatabaseConnector, Andromeda, FeatureExtraction, Cyclops, and CohortMethod. Some packages (including the skeletons) still need some minor tweaks, but after that we should be able to release everything and have full support for 64-bit integers.
So I recommend using BIGINTS in the CDM where appropriate. I would ask that concept IDs remain 32-bit integers, or else FeatureExtraction has a problem.