[R] package installation for Windows 7

[Joris Meys]

Hi,

I am running Windows 7 and R 2.11.1, and everything is installing just
fine for me. Did you install R in the "Program Files" folder? If so,
uninstall and try to re-install R in another folder (e.g.
c:\R\R2.11.1\ like on my computer). I noticed in the past that the
access control of Windows treats the "Program Files" folder different
compared to other folders.

Cheers
Joris

On Thu, Jul 8, 2010 at 1:15 PM, Dave Bickel
<davidbickel.com+reply at gmail.com> wrote:
> Neither biocLite nor the GUI menus can install packages on my system. 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
>
> --
> David R. Bickel, PhD
> Associate Professor
> Ottawa Institute of Systems Biology
> Biochem., Micro. and I. Department
> Mathematics and Statistics Department
> University of Ottawa
> 451 Smyth Road
> Ottawa, Ontario K1H 8M5
>
> http://www.statomics.com
>
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> the door to the OISB area.)
> Lab Tel.: (613) 562-5800 ext. 8304
> Lab Room: RGN 4501T
>
> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>



-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control

tel : +32 9 264 59 87
Joris.Meys at Ugent.be
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