[R] package installation for Windows 7

[David Bickel]

Thanks, Joris. Your suggestion solved the problem without requiring me 
to run R as an administrator.

Best regards,
David


On 08/07/2010 8:45 AM, Joris Meys wrote:
> 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
>>
>> Office Tel: (613) 562-5800 ext. 8670
>> Office Fax: (613) 562-5185
>> Office Room: RGN 4510F (Follow the signs to the elevator, and take it to the
>> fourth floor. Turn left and go all the way to the end of the hall, and enter
>> 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
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>      
>
>
>