[BioC] How to download package bundles?

Peter Baker (CMIS, St Lucia) Peter.Baker at csiro.au
Wed Jul 28 09:49:17 CEST 2004


I simply want to download Win32 sources at work for a home machine. My
work machine is a linux box with Bioconductor installed

Just wondering why this doesn't work

> library(reposTools)
> rep22 <- repositories(recurse = TRUE)
and I then select the windows repository

I can download a single package, eg

> download.packages2("edd",repEntry=rep22,type="Win32")
Note: destDir parameter missing, using current directory
[1] "Attempting to download edd from http://www.bioconductor.org/repository/release1.4/package/Win32"
[1] "Download complete."
[1] "/home/baker/tmp/R-forhome/edd_1.4.0.zip"

but when I try and download all packages I get

> download.packages2(repEntry=rep22,type="Win32") Note: destDir parameter missing, using current directory
Note: pkgs parameter missing, downloading all packages in repository

and nothing happens.

Alternatively, is there an easy way to get a vector of package
listings and define all packages explicitly. Its not obvious to me how
to do this e.g.

> rep22 at repdatadesc
      pkgs                 vers   types
 [1,] AnnBuilder           1.4.2  Source, Win32
 [2,] Biobase              1.4.15 Win32
 [3,] Biostrings           1.0.0  Win32
 ................... 75 other packages deleted

> rep22 at repdatadesc["pkgs"]


Comments welcome



Dr Peter Baker, Statistician (Bioinformatics/Genetics),
CSIRO Mathematical & Information Sciences, Queensland Bioscience Precinct
306 Carmody Road, St Lucia Qld 4067.   Australia.
Email: <Peter.Baker at csiro.au>
WWW: http://www.cmis.csiro.au/Peter.Baker/
Phone:+61 7 3214 2210   Fax:+61 7 3214 2900

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