Can you confirm you have write permissions on:

 ‘\\smb.pass.psu.edu/nsa1/My Documents/R/win-library/3.0’

It all suggests that your previous version of BiocInstaller is installed
there and without write permissions the installer cannnot remove it for you
to proceed with the upgrade...

b


2014/1/14 Naomi Altman <naomi@stat.psu.edu>

>  sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> > source("http://bioconductor.org/biocLite.R")
> Installing package into ‘\\smb.pass.psu.edu/nsa1/MyDocuments/R/win-library/3.0’
> (as ‘lib’ is unspecified)
> trying URL 'http://www.bioconductor.org/packages/2.12/bioc/bin/
> windows/contrib/3.0/BiocInstaller_1.10.4.zip'
> Content type 'application/zip' length 50486 bytes (49 Kb)
> opened URL
> downloaded 49 Kb
>
> Warning: cannot remove prior installation of package ‘BiocInstaller’
>
> The downloaded binary packages are in
> C:\Users\nsa1\AppData\Local\Temp\RtmpIN7Ew0\downloaded_packages
> 'biocLite.R' failed to install 'BiocInstaller', use
> 'install.packages("BiocInstaller",
> repos="http://www.bioconductor.org/packages/2.12/bioc")'
> > install.packages("BiocInstaller",
> + repos="http://www.bioconductor.org/packages/2.12/bioc")
> Installing package into ‘\\smb.pass.psu.edu/nsa1/MyDocuments/R/win-library/3.0’
> (as ‘lib’ is unspecified)
> trying URL 'http://www.bioconductor.org/packages/2.12/bioc/bin/
> windows/contrib/3.0/BiocInstaller_1.10.4.zip'
> Content type 'application/zip' length 50486 bytes (49 Kb)
> opened URL
> downloaded 49 Kb
>
> Warning: cannot remove prior installation of package ‘BiocInstaller’
>
> The downloaded binary packages are in
> C:\Users\nsa1\AppData\Local\Temp\RtmpIN7Ew0\downloaded_packages
> >
>
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