From mtmorgan at fhcrc.org  Sat Jun 11 05:50:53 2011
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Fri, 10 Jun 2011 20:50:53 -0700
Subject: [Rd] CRAN package with dependencies on Bioconductor
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On 06/10/2011 05:46 PM, Kornelius Rohmeyer wrote:
> Dear Martin,
>
> thanks for your response.
>
>>> 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.
>>
>> biocLite is returning the correct package -- graph 1.28.0. graph 1.30 did
>> not come in to existence until the most recent release, 2011-04-13,
>> approximately when R-2.13 became the current release version.
>>
>> CRAN is building packages with the current release, R-2.13, for which
>> biocLite and install.packages both (correctly) return graph 1.30.
>
> I doubt this, i.e. CRAN is also still building packages for R 2.12 -
> and is using graph 1.30 for this as far as I understand it (instead of
> 1.28).

I'm not intimately familiar with CRAN's build system, so perhaps I 
mis-spoke; Bioconductor packages are versioned in synchrony with R 
releases. If your package requires graph >= 1.30, specify that in the 
DESCRIPTION. If your users want features introduced when your package 
requires graph >= 1.30, direct them to use R >= 2.13.

Martin

>>> Are there ways to make dependencies on Bioconductor less complicated?
>>
>> Use the current version of R.
>
> So you agree that it is impossible to give a reasonable instruction
> install such binary packages for older versions of R like the four
> month old R 2.12? (Reasonable means without manual installation of
> packages in the correct versions - where the correct versions have to
> be found out by the maintainer.)
>
> Best regards, Kornelius.


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[Rd] CRAN package with dependencies on Bioconductor
Martin Morgan