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
Location: M1-B861
Telephone: 206 667-2793
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