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R package with CRAN and Bioconductor dependencies

I have an R package stored on a local git server. This package has a series of dependecies - packages from both CRAN and Bioconductor. Using the devtools package, I can install from git directly:

library(devtools)
install_git("http://mygitserver.com/username/reponame")

I have noticed that this installation process fails to install all of the Bioconductor dependencies, but all of the CRAN dependencies are installed correctly.

How can I set up the package's dependencies (in the DESCRIPTION file) so that all of the Bioconductor package dependencies are also installed correctly. I've noticed this is not a problem when the packages are hosted on a Bioconductor mirror and installed via biocLite(), which suggests that perhaps I could resolve this by listing a set of mirrors for install.packages() to search through before declaring that the package cannot be found. Is there a way to get all of these dependencies automatically?

Solution

  • The short answer: setRepositories(ind=1:2)

    tl;dr

    The documentation for setRepositories tells us that the "default list of known repositories is stored in the file 'R_Home/etc/repositories'". We can track this down a couple of ways, but for convenience, let's read the table of repositories into R (this will cut off all of the commented documentation in that file, but you can pull that up with readLines if you're interested.

    read.table(file.path(R.home(), "etc", "repositories"), sep = "\t")

                             menu_name                                 URL default source win.binary mac.binary
CRAN                              CRAN                              @CRAN@    TRUE   TRUE       TRUE       TRUE
BioCsoft                 BioC software                %bm/packages/%v/bioc   FALSE   TRUE       TRUE       TRUE
BioCann                BioC annotation     %bm/packages/%v/data/annotation   FALSE   TRUE       TRUE       TRUE
BioCexp                BioC experiment     %bm/packages/%v/data/experiment   FALSE   TRUE       TRUE       TRUE
BioCextra                   BioC extra               %bm/packages/%v/extra   FALSE   TRUE       TRUE       TRUE
CRANextra                CRAN (extras)  http://www.stats.ox.ac.uk/pub/RWin   FALSE   TRUE       TRUE       TRUE
Omegahat                      Omegahat           http://www.omegahat.org/R   FALSE   TRUE      FALSE      FALSE
R-Forge                        R-Forge        http://R-Forge.R-project.org   FALSE   TRUE       TRUE       TRUE
rforge.net                  rforge.net               http://www.rforge.net   FALSE   TRUE       TRUE       TRUE
CRANextra[https]  CRAN (extras, https) https://www.stats.ox.ac.uk/pub/RWin   FALSE   TRUE       TRUE       TRUE
R-Forge[https]         R-Forge [https]       https://R-Forge.R-project.org   FALSE   TRUE       TRUE       TRUE
rforge.net[https]   rforge.net [https]              https://www.rforge.net   FALSE   TRUE       TRUE       TRUE

    Imagine that each row has an index number. When you call setRepositories(ind = 1:2) you are telling R to look at the repositories in rows 1 and 2.