[Rd] [Suggestion] Installation of CRAN packages that depend on Bioconductor packages

From: Renaud Gaujoux <renaud_at_mancala.cbio.uct.ac.za>
Date: Thu, 28 Jun 2012 13:39:13 +0200


Hi,

as far as I know, calling a plain:

install.packages('packageA')

with packageA having a dependency to packageB from Bioconductor will not complete without having a Bioc mirror setup in options('repos') or specifying it in argument 'repos'.

CRAN/R-forge checks resolve such dependencies automatically. Would it be possible (and not problematic) to also resolve such standard dependencies at install time (in fact build time) and automatically append a Bioc mirror to repos within install.package (if none is already defined)?
The dependency would be hence completely transparent, which would simplify the installation of such packages, as the user would not need to know that a repository other than CRAN is required. Resolution could make use of the function chooseBioCMirror to ask the user to select her preferred mirror, as it is done for the CRAN mirror.

Thank you.

Renaud

-- 
Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa

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Received on Thu 28 Jun 2012 - 11:43:28 GMT

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