[Rd] CRAN package with dependencies on Bioconductor

Kornelius Rohmeyer kornelius.rohmeyer at small-projects.de
Sat Jun 11 09:10:28 CEST 2011

2011/6/11 Prof Brian Ripley <ripley at 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.

Thanks for the notice! But if I am not wrong, a version of my package
that was published on May 26 and build therefore after the time period
specified by you still suffers from these version incompatibilities.
(Nevertheless it is of course possible that the problem is only caused
by the migration to Bioconductor and in this case less problematic and
only unfortunate in this one case). Perhaps the version downgrade of
the graph package caused problems?

So you say that the versions of Bioconductor packages on CRAN for
binary builds are already normally the same as you would get by
installing them as binaries from Bioconductor? (And btw. is there a
way to find out which versions of the dependent packages were used for
building a certain binary package?)

Thanks and best regards, Kornelius.

> 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)
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