Installing lumi and hdrcde

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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")
This can easily be solved by using the correct spelling for "bioconductor".

Uwe Ligges
Fehler in file(filenaReme, "r", encoding = encoding) :
   kann Verbindung nicht ?ffnen
Zus?tzlich: Warnmeldung:
In file(filename, "r", encoding = encoding) :
   kann 'bioconductur.org' nicht aufl?sen
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 ge?ffnet
==================================================
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?

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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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

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 ?ffnen
Zus?tzlich: Warnmeldung:
In file(filename, "r", encoding = encoding) :
   kann 'bioconductur.org' nicht aufl?sen
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 ge?ffnet
==================================================
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]]

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

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