From kornelius.rohmeyer at small-projects.de  Sat Jun 11 01:04:52 2011
From: kornelius.rohmeyer at small-projects.de (Kornelius Rohmeyer)
Date: Sat, 11 Jun 2011 01:04:52 +0200
Subject: [Rd] CRAN package with dependencies on Bioconductor
In-Reply-To: <BANLkTinzAC44xnkHzVk+=BK3qaPYPQqtkA@mail.gmail.com>
References: <BANLkTinzAC44xnkHzVk+=BK3qaPYPQqtkA@mail.gmail.com>
Message-ID: <BANLkTi=aOE4hPt9YRw=PqXkpk2Jcv8rRqA@mail.gmail.com>

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



[Rd] CRAN package with dependencies on Bioconductor
Kornelius Rohmeyer