Dear all,

for a CRAN-package that depends on another Bioconductor-package I find two
things annoying and would like to know whether there are some workarounds:

1) Is there some inevitable problem that install.packages does not install
uninstalled packages (on which the specified package depends) also from
Bioconductor (in the correct version)?

2) In my understanding (please correct me if I'm wrong!) CRAN uses
bioconductor packages in another version than biocLite would install. For
example:

Our package gMCP depends on the package graph that has recently switched to
the bioconductor repositories. But even the following commands will fail
(i.e. install incompatible versions) for R 2.12 under Windows (and most
likely MacOS):

source("http://www.bioconductor.org/biocLite.R")
biocLite("graph")
install.packages("gMCP")

This results in errors like the following:

> BonferroniHolmGraph(2)
Error in validObject(.Object) :
  invalid class "graphMCP" object: superclass "graphBase" not defined in the
environment of the object's class

The superclass graphBase is introduced in graph 1.30. In my understanding
the problem is that our package gMCP is build on CRAN for R 2.12 with the
package graph in version 1.30. Unfortunately biocLite installs
graph_1.28.0.zip for R 2.12.

Are there ways to make dependencies on Bioconductor less complicated?

Thanks and best regards, Kornelius

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