For RStudio the chosen way of storing packages with each project codebase is 'packrat'. This tool allows all of the packages associated with a script or set of scripts to be saved within a project area.
Some of the background and reasons for using packrat can be found here - https://rstudio.github.io/packrat/, but within DataLabs is allows us to keep all user content - both code, data & packages on the allocated data stores.