[BioC] Installation Error with Bioconductor on R

[Steve Lianoglou]

Hi,

On Jun 19, 2008, at 10:52 PM, A A wrote:

> Hi, I am trying to install Bioconductor onto R version 2.7.0 for  
> Windows.  I installed R, then followed the instructions on:
> http://www.bioconductor.org/download, which state that you should  
> type the following:
>
> source("http://bioconductor.org/biocLite.R")biocLite()
>
> When I do that, I get the following error:
>
> Running biocinstall version 2.2.9 with R version 2.7.0 Your version  
> of R requires version 2.2 of BioConductor.Will install the following  
> packages: [1] "affy"         "affydata"     "affyPLM"       
> "annaffy"      "annotate"     [6] "Biobase"      "Biostrings"    
> "DynDoc"       "gcrma"        "genefilter"  [11] "geneplotter"   
> "hgu95av2.db"  "limma"        "marray"       "matchprobes" [16]  
> "multtest"     "ROC"          "vsn"          "xtable"        
> "affyQCReport"
>
> Anything that, everything I install after this gives me the same  
> error.  I tried uninstalling R 2.7.0 and installing R 2.6.2, and  
> performing the same commands, as above, but the same thing  
> happens.Does anyone have any suggestions?
> Thanks,A

That's not an error, it's just telling you what it's doing. As you let  
it run, you should see periodic messages telling you that it's saving  
the downloads in some temp directory (that's what it does on my mac,  
so I'm guessing windows is the same).

When this process finishes, you can then load any of those  
bioconductor packages and you're good to go.

For instance, after it's finished you can type:

 > library('affy')
 > openVignette()

And you'll see a list of tutorials for the affy package that you can  
start working through.

HTH,
-steve