Re: [Rd] CRAN package with dependencies on Bioconductor

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Sat, 11 Jun 2011 07:07:19 +0100 (BST)

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
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
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>
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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

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