[BioC] preprocessCore load problem in R

[Dan Tenenbaum]

On Tue, Sep 3, 2013 at 12:52 PM, Rao,Xiayu <XRao at mdanderson.org> wrote:
> Hello all,
>
> Has anyone encountered the same problem as mine? library(preprocessCore) does not work for me.
>
>> source("http://bioconductor.org/biocLite.R")
> Bioconductor version 2.12 (BiocInstaller 1.10.3), ?biocLite for help
>
>> biocLite("preprocessCore")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1.
> Installing package(s) 'preprocessCore'
> trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/preprocessCore_1.22.0.zip'
> Content type 'application/zip' length 204423 bytes (199 Kb)
> opened URL
> downloaded 199 Kb
>
> package 'preprocessCore' successfully unpacked and MD5 sums checked
>
> The downloaded binary packages are in
>         C:\Users\xrao\AppData\Local\Temp\Rtmp8eMyPl\downloaded_packages
> Warning message:
> installed directory not writable,

This means the directory you are trying to install in is not writable
by the user that R is running as. Since you're on Windows, try running
R as an administrator. Right-click on the R icon and choose "Run as
administrator".

Dan


>  cannot update packages 'class', 'foreign', 'lattice', 'MASS', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial'
>
>> library(preprocessCore)
> Error in library(preprocessCore) :
>   there is no package called 'preprocessCore'
>
> I am using the latest version of R.  R version 3.0.1 (2013-05-16) -- "Good Sport"
>
>
> Thanks a lot in advance!
>
> Best,
> Xiayu
>
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>
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