[R] Installing lumi and hdrcde

[Martin Morgan]

On 09/05/2012 02:41 AM, Hermann Norpois wrote:
> To whom it may concern.
>
> As I would like to analyse some array data I was keen on downloading the
> lumi package that depends obviously on hdrcde that is not available for r
> 2.12.1. I did not find instructions to solve or circumvent this problem.
> Installing hdrcde by hand did not work either. It was not detected by
>> (.packages(all.available=TRUE))
> if installed in the R library.
>
> Thanks
> Hermann Norpois
>
> This was my try to install the lumi package:
>
>> source ("http://bioconductur.org/biocLite.R")
> Fehler in file(filenaReme, "r", encoding = encoding) :
>    kann Verbindung nicht öffnen
> Zusätzlich: Warnmeldung:
> In file(filename, "r", encoding = encoding) :
>    kann 'bioconductur.org' nicht auflösen
>> source ("http://bioconductor.org/biocLite.R")
> BiocInstaller version 1.2.1, ?biocLite for help
>> biocLite("lumi")
> BioC_mirror: 'http://www.bioconductor.org'
> Using R version 2.14, BiocInstaller version 1.2.1.
> Installing package(s) 'lumi'
> Installing package(s) into ‘/home/hnorpois/R/i686-pc-
> linux-gnu-library/2.14’
> (as ‘lib’ is unspecified)
> Warnung: dependency ‘hdrcde’ is not available
> versuche URL '
> http://www.bioconductor.org/packages/2.9/bioc/src/contrib/lumi_2.6.0.tar.gz'
> Content type 'application/x-gzip' length 11386679 bytes (10.9 Mb)
> URL geöffnet
> ==================================================
> downloaded 10.9 Mb
>
> ERROR: dependency ‘hdrcde’ is not available for package ‘lumi’
> * removing ‘/home/hnorpois/R/i686-pc-linux-gnu-library/2.14/lumi’

If I use R-2.14 and

   install.packages("hdrcde", repos="http://cran.fhcrc.org")

I get

In getDependencies(pkgs, dependencies, available, lib) :
   package 'hdrcde' is not available (for R version 2.14.0 alpha)

but if I use R-2.15 the package installs correctly. Likewise with 
biocLite("lumi").

So I think the easiest solution is to use a current version of R.

Please ask questions about Bioconductor packages on the Bioconductor 
mailing list http://bioconductor.org/help/mailing-list/

Martin



>
> The downloaded packages are in
>      ‘/tmp/RtmpMNrvTz/downloaded_packages’
> Warnmeldungen:
> 1: In install.packages(pkgs = pkgs, repos = repos, ...) :
>    installation of package ‘lumi’ had non-zero exit status
> 2: 'rgl' cannot be updated, installed directory '/usr/lib/R/site-library'
> not
>    writeable
>
> 	[[alternative HTML version deleted]]
>
>
>
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