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 the packages which are deposited under CRAN not for bioconductor packages. besides, it has a package dependencies error for Mac OS: check log for Mac OS

what could be the problem? and how could I fixed it?

Kind regards,

Answer 1

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 2

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.