From ripley at stats.ox.ac.uk  Thu May 21 08:17:29 2009
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Thu, 21 May 2009 07:17:29 +0100 (BST)
Subject: [Rd] install.packages now intentionally references .Rprofile?
In-Reply-To: <6ph4ovf1gi0.fsf@gopher4.fhcrc.org>
References: <6ph4ovf1gi0.fsf@gopher4.fhcrc.org>
Message-ID: <alpine.LFD.2.00.0905210715100.30855@gannet.stats.ox.ac.uk>

On Wed, 20 May 2009, Martin Morgan wrote:

> A post on the Bioconductor mailing list
>
>  https://stat.ethz.ch/pipermail/bioconductor/2009-May/027700.html
>
> suggests that install.packages now references .Rprofile (?), whereas
> in R-2-8 it did not. Is this intentional?

Yes.  And in fact it did in earlier versions, to find the default 
library into which to install.

>
> The example is, in .Rprofile
>
>  library(utils)
>  install.packages("Biobase",
>                   repos="http://bioconductor.org/packages/2.4/bioc")
>
> then starting R from the command line results in repeated downloads
> of Biobase
>
> mtmorgan at mm:~/tmp> R --quiet
> trying URL
> 'http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz'
> Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb)
> opened URL
> ==================================================
> downloaded 1.9 Mb
>
> trying URL
> 'http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz'
> Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb)
> opened URL
> ==================================================
> downloaded 1.9 Mb
>
> ^C
> Execution halted
>
>> sessionInfo()
> R version 2.9.0 Patched (2009-05-20 r48588)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> Martin
> -- 
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
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)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] install.packages now intentionally references .Rprofile?
Prof Brian Ripley