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

Wed Oct 12 18:17:11 CEST 2011

Hi Sarah,

Comments inline.

On 10/12/2011 11:24 AM, Sarah Little [guest] 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()"

In this workflow, the terms 'cdf', 'probe' and 'annotation' are used as 
general descriptive terms, not as actual package names. The correct cdf 
package will be installed automagically by the affy package, so you 
don't have to worry about that.

If you want to install the annotation package, note that the name of the 
package will be hgu133a2.db, so something like

library(BiocInstaller)
biocLite("hgu133a2.db")

will install it for you.

The probe package will be called hgu133a2probe, and can be installed in 
a similar fashion.

>
> 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

This part ^^^^^^^ is where the correct cdf package is installed.

>
>
> 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

This looks like you copied the whole line, including the 'R >' prompt 
and then pasted into your R session. You don't want to include that 
first bit, as what this line translates to in 'R speak' is:

Is some object 'R' greater than an object 'eset', which is created by 
running mas5() on an object called 'Data'.

Since R couldn't find this 'R' object, it spit out the error saying it 
couldn't find it.

Best,

Jim

>> 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 â?~cdfâ?T 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 â?~biocinstallâ?T
> 2: In safeSource() : Redefining â?~biocinstallPkgGroupsâ?T
> 3: In safeSource() : Redefining â?~biocinstallReposâ?T
>> 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 â?~probeâ?T 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 â?~annotationâ?T is not available (for R version 2.13.2)
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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