[R] package installation for Windows 7

[Duncan Murdoch]

On 08/07/2010 7:15 AM, Dave Bickel wrote:
> Neither biocLite nor the GUI menus can install packages on my system. 
>   

This is probably a permissions problem.  Are you running R as an 
administrator when you try the install?  If not, you won't be able to 
install to the default location, but you should be able to set up your 
own library somewhere else, and install there.

The error message should be fixed; we shouldn't give

Error in if (ok) { : missing value where TRUE/FALSE needed


but I doubt if that's the source of your problem.

BTW, in future Bioconductor questions should go to their list.  In this 
case it looks as though it's not a BioC problem, but that just means 
there's no need to list all the biocLite.R material at the start:  short 
simple bug reports are easier to deal with.

Duncan Murdoch

> Here is relevant output:
>
>  > version
> _
> platform i386-pc-mingw32
> arch i386
> os mingw32
> system i386, mingw32
> status
> major 2
> minor 11.1
> year 2010
> month 05
> day 31
> svn rev 52157
> language R
> version.string R version 2.11.1 (2010-05-31)
>  > source("http://bioconductor.org/biocLite.R")
> BioC_mirror = http://www.bioconductor.org
> Change using chooseBioCmirror().
>  > biocLite("ALL")
> Using R version 2.11.1, biocinstall version 2.6.7.
> Installing Bioconductor version 2.6 packages:
> [1] "ALL"
> Please wait...
>
> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
> argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
> Error in if (ok) { : missing value where TRUE/FALSE needed
>  > source("http://bioconductor.org/biocLite.R")
> BioC_mirror = http://www.bioconductor.org
> Change using chooseBioCmirror().
> Warning messages:
> 1: In safeSource() : Redefining ‘biocinstall’
> 2: In safeSource() : Redefining ‘biocinstallPkgGroups’
> 3: In safeSource() : Redefining ‘biocinstallRepos’
>  > biocLite()
> Using R version 2.11.1, biocinstall version 2.6.7.
> Installing Bioconductor version 2.6 packages:
> [1] "affy" "affydata" "affyPLM" "affyQCReport"
> [5] "annaffy" "annotate" "Biobase" "biomaRt"
> [9] "Biostrings" "DynDoc" "gcrma" "genefilter"
> [13] "geneplotter" "GenomicRanges" "hgu95av2.db" "limma"
> [17] "marray" "multtest" "vsn" "xtable"
> Please wait...
>
> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
> argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
> Error in if (ok) { : missing value where TRUE/FALSE needed
>  > biocLite()
> Using R version 2.11.1, biocinstall version 2.6.7.
> Installing Bioconductor version 2.6 packages:
> [1] "affy" "affydata" "affyPLM" "affyQCReport"
> [5] "annaffy" "annotate" "Biobase" "biomaRt"
> [9] "Biostrings" "DynDoc" "gcrma" "genefilter"
> [13] "geneplotter" "GenomicRanges" "hgu95av2.db" "limma"
> [17] "marray" "multtest" "vsn" "xtable"
> Please wait...
>
> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
> argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
> Error in if (ok) { : missing value where TRUE/FALSE needed
>  > library(Biobase)
> Error in library(Biobase) : there is no package called 'Biobase'
>  > biocLite("Biobase")
> Using R version 2.11.1, biocinstall version 2.6.7.
> Installing Bioconductor version 2.6 packages:
> [1] "Biobase"
> Please wait...
>
> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
> argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
> Error in if (ok) { : missing value where TRUE/FALSE needed
>  > source("http://bioconductor.org/biocLite.R")
> BioC_mirror = http://www.bioconductor.org
> Change using chooseBioCmirror().
> Warning messages:
> 1: In safeSource() : Redefining ‘biocinstall’
> 2: In safeSource() : Redefining ‘biocinstallPkgGroups’
> 3: In safeSource() : Redefining ‘biocinstallRepos’
>  > biocLite("Biobase")
> Using R version 2.11.1, biocinstall version 2.6.7.
> Installing Bioconductor version 2.6 packages:
> [1] "Biobase"
> Please wait...
>
> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
> argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
> Error in if (ok) { : missing value where TRUE/FALSE needed
>
>  > utils:::menuInstallLocal() # "Install package(s) from local zip 
> files..."
> Error in if (ok) { : missing value where TRUE/FALSE needed
>
>  > utils:::menuInstallPkgs() # "Install package(s)..."
> --- Please select a CRAN mirror for use in this session ---
> Error in if (ok) { : missing value where TRUE/FALSE needed
>
>
> I would appreciate any assistance.
>
> David
>
>