[BioC] Installing packages on R v2.13.2, OSX multiple warning messages

[Sarah Little [guest]]

Dear All,

Firstly, I am new to both R and bioconductor, but I have tried to solve my problem with google, R FAQ and bioconductor help pages and not got anywhere.

I have only installed R today, using this download
http://cran.ma.imperial.ac.uk/bin/macosx/

I'm trying to run the affy package to analyse some HG-U133A2 data....

and have come across an error:
"Error in R > eset <- mas5(Data) : object 'R' not found"

Whilst trying to work out why I get the above message, and what might be missing I realise the following (from the sample workflow page):
"Affymetrix 3'-biased Arrays

affy, gcrma, affyPLM
Require cdf package, probe package and annotation package
All these packages are available from Bioconductor via biocLite()"

However when trying to install all three of these packages I get the warning message
"package is not available (for R version 2.13.2)"

In the package list http://bioconductor.org/packages/release/bioc/
None of these three packages are listed for me to see if they run on OSX.

Therefore I think I might be confused about these three packages and the earlier error I received running affy.


Any clarification gratefully received. 
Thanks in advance for your help.
Kind regards,

-Sarah

 -- output of sessionInfo(): 

> library(affy)
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

> Data <- ReadAffy()
> eset <- rma(Data)
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13
trying URL 'http://bioconductor.org/packages/2.8/data/annotation/bin/macosx/leopard/contrib/2.13/hgu133a2cdf_2.8.0.tgz'
Content type 'application/x-gzip' length 1744432 bytes (1.7 Mb)
opened URL
==================================================
downloaded 1.7 Mb


The downloaded packages are in
	/var/folders/uF/uFWwo07rEmKgKopLFvaXGk+++TI/-Tmp-//RtmpgL0vGe/downloaded_packages
Background correcting
Normalizing
Calculating Expression
> eset <- expresso(Dilution, normalize.method="qspline", bgcorrect.method="rma",pmcorrect.method="pmonly",
+ summary.method="liwong")
Error in expresso(Dilution, normalize.method = "qspline", bgcorrect.method = "rma",  : 
  object 'Dilution' not found
> R> eset <- mas5(Data)
background correction: mas 
PM/MM correction : mas 
expression values: mas 
background correcting...done.
22277 ids to be processed
|                    |
|####################|
Error in R > eset <- mas5(Data) : object 'R' not found
> biocLite("cdf")
Error: could not find function "biocLite"
> source("http://www.bioconductor.org/biocLite.R")
BioC_mirror = http://bioconductor.org
Change using chooseBioCmirror().
> biocLite("cdf")
Using R version 2.13.2, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] "cdf"
Please wait...

Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘cdf’ is not available (for R version 2.13.2)
> biocLIte("probe")
Error: could not find function "biocLIte"
> source("http://www.bioconductor.org/biocLite.R")
BioC_mirror = http://bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
> biocLite("probe")
Using R version 2.13.2, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] "probe"
Please wait...

Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘probe’ is not available (for R version 2.13.2)
> biocLite("annotation")
Using R version 2.13.2, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] "annotation"
Please wait...

Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘annotation’ is not available (for R version 2.13.2)
> 


--
Sent via the guest posting facility at bioconductor.org.