Re: [Rd] CRAN package with dependencies on Bioconductor

From: Kornelius Rohmeyer <kornelius.rohmeyer_at_small-projects.de>
Date: Sat, 11 Jun 2011 01:04:52 +0200

I'm sorry for sending a wrongly formated mail before. This is the missing text:

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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