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,
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.