From renaud at mancala.cbio.uct.ac.za  Thu Jun 28 13:39:13 2012
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Thu, 28 Jun 2012 13:39:13 +0200
Subject: [Rd] [Suggestion] Installation of CRAN packages that depend on
 Bioconductor packages
Message-ID: <4FEC4261.70208@cbio.uct.ac.za>

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



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