CRAN Package Depends on Bioconductor Package Installing error

Question

I manage the Depends, suggests and imports of the description file. and finally I submit my package to CRAN. But during installation the package, it only install th

Answer 1

This is not documented anywhere but the trick is that you add a line that says biocViews: in your DESCRIPTION file (yes, it ends with a colon and then no need to list anything, you can keep it blank). Then R will know to check bioconductor repositories for the package requirements.

Answer 2

In R 3.0.2, the following works:

setRepositories(ind=1:2)

At the time of this writing, the value ind can take a vector with values between 1 and 8, and the following meaning:

1:   CRAN
2:   BioC software
3:   BioC annotation
4:   BioC experiment
5:   BioC extra
6:   Omegahat
7:   R-Forge
8:   rforge.net

This list is obtained by calling setRepositories(graphics=F), which also allows interactively choosing the repositories to be installed from.

Answer 3

There is no mechanism by which install.packages() can install from Bioconductor by default in R (at least not by default, I haven't checked if BioC has the repo infrastructure to allow it if called correctly). [See the comment from Martin Morgan (below) wherein instructions can be found on how to configure R so that install.packages() can install from the Bioconductor repositories.]

To install a Bioconductor package one normally does:

source("http://bioconductor.org/biocLite.R")
biocLite("limma")

which needs to be done independently of install.packages().

The error with Mac OS X checking is potentially a configuration error on that particular server. As @DWin says, you should take this up with CRAN to get to the root of that particular problem. To the best of my knowledge CRAN is supposed to have all the Bioconductor packages installed.