From ripley at stats.ox.ac.uk  Sat Jun 11 08:07:19 2011
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Sat, 11 Jun 2011 07:07:19 +0100 (BST)
Subject: [Rd] CRAN package with dependencies on Bioconductor
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	<4DF2E61D.8080009@fhcrc.org>
Message-ID: <alpine.LFD.2.02.1106110702420.24811@gannet.stats.ox.ac.uk>

Note that until May 8 graph was a CRAN packge and the current version 
was 1.30.0.  So of course CRAN binary packages built between April 26 
and May 8 were built against the current CRAN version of graph, for 
any version of R.

On Fri, 10 Jun 2011, Martin Morgan wrote:

> 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.
>
>
> -- 
> Computational Biology
> Fred Hutchinson Cancer Research Center
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] CRAN package with dependencies on Bioconductor
Prof Brian Ripley