[BioC] repositories2

[Jeff Gentry]

> Is there an easy way to override the built-in options()$repositories2 
> list from an .Rprofile file to use a locally mirrored repository?

Currently what should happen is if you have 'repositories2' defined before
loading reposTools, any value that reposTools wants to set will not be
overwritten.  For instance, if before loading reposTools you set:

> options(repositories2=c(CRAN="http://cran.r-project.org",
BIOCData="http://www.local.mirror.org"))

Then upon loading reposTools you should see:

 getOption("repositories2")
                                                       CRAN 
                                "http://cran.r-project.org" 
                                                   BIOCData 
                              "http://www.local.mirror.org" 
                                                 BIOCRel1.3 
"http://www.bioconductor.org/repository/release1.3/package" 
                                                  BIOCDevel 
     "http://www.bioconductor.org/repository/devel/package" 
                                                BIOCDevData 
          "http://www.bioconductor.org/data/metaData-devel" 
                                                 BIOCExdata 
      "http://www.bioconductor.org/data/experimental/repos" 
                                                BIOCCourses 
           "http://www.bioconductor.org/repository/Courses" 
                                                    BIOCcdf 
           "http://www.bioconductor.org/data/cdfenvs/repos" 
                                                 BIOCprobes 
         "http://www.bioconductor.org/data/probes/Packages" 
                                               BIOCOmegahat 
          "http://www.bioconductor.org/repository/Omegahat" 

A good question is if this is the proper behavior, or should reposTools
detect that a 'repositories2' option exists and simply not change anything
in it instead of only leaving alone the similar entries.

-J