Checkpoint only allows specifying that all packages as they existed on a particular data in CRAN be downloaded and utilized within a project. This is limiting in that an R developer may want to utilize very specific versions of packages that span multiple epochs.

I would really like to see R develop functionality akin to Maven or SBT, such that an R developer can explicitly specify the exact versions of all dependencies, which will then be installed at the first run.

That's the goal of packrat. (But it's still a work in progress)