[R] Installation Error with Bioconductor on R

Martin Morgan mtmorgan at fhcrc.org
Thu Jun 19 23:10:55 CEST 2008


Ask on the bioconductor mailing list, following the 'mailing lists' link 
on the front page http://bioconductor.org


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"

the command biocLite() installs a number of packages; the above message 
is NOT an error, but an information message saying that the packages 
mentioned above are to be installed. Likely these packages are retrieved 
from the internet and installed on your computer, there should be quite 
a bit more output before returning to R, or are you saying that R stops 
working after the message above?

> Anything that 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
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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