From kornelius.rohmeyer at small-projects.de  Sat Jun 11 06:29:27 2011
From: kornelius.rohmeyer at small-projects.de (Kornelius Rohmeyer)
Date: Sat, 11 Jun 2011 06:29:27 +0200
Subject: [Rd] CRAN package with dependencies on Bioconductor
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2011/6/11 Martin Morgan <mtmorgan at fhcrc.org>:
> 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.

I understand this. But my package does not require graph >= 1.30.
(And if I install the source packages everything is always fine.)
The problem is again that R 2.12 installs graph 1.28
but the CRAN packages for R 2.12 are build for graph 1.30.
So the default binary packages are incompatible for R 2.12.

Best regards, Kornelius.

>
> 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
>
> Location: M1-B861
> Telephone: 206 667-2793
>



[Rd] CRAN package with dependencies on Bioconductor
Kornelius Rohmeyer