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

[Kasper Daniel Hansen]

You should not copy the "R>" part of whatever document you are using.
The beginning "R>" just refers to the R prompt.  Sometimes the R is
left out, like ">" and in that case you should also not copy the ">".

Kasper

On Wed, Oct 12, 2011 at 11:24 AM, Sarah Little [guest]
<guest at bioconductor.org> wrote:
>
> 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.
>
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