[BioC] [Rd] enabling reproducible research & R package management & install.package.version & BiocLite

[Geoff Jentry]

On Tue, 5 Mar 2013, Cook, Malcolm wrote:
> Thus, I might rather consider an approach that at 'publish' time tarzips 
> up a copy of the R package dependencies based on a config file defined 
> from sessionInfo and caches it in the project directory.

If you had a separate environment for every project, each with its own R 
installation and R installation lib.loc this becomes rather easy. For 
instance, something like this:

myProject/
    projectRInstallation/
       bin/
         R
       library/
         Biobase
         annotate
         .....
       ....
    projectData/
    projectCode/
    projectOutput/

The directory structure would likely be more complicated than that but 
something along those lines. This way all code, data *and* compute 
environment are always linked together.

-J