[R] package installation for Windows 7

[Duncan Murdoch]

David Bickel wrote:
>  Now that I have installed R outside "Program files" to get past the
> permissions problem, there are packages I can only access from certain
> working directories:
>
>   
>> setwd("U:/Calc/zTemp") # "U:" points to a USB hard drive
>> library(splines) # ok
>> library(locfdr)
>>     
> Error in library(locfdr) : there is no package called 'locfdr'
>   
>> setwd("C:/Users/dbickel/Documents")
>> library(locfdr) # ok
>>     
>
> The same error occurs whether or not I run R as administrator. Is there a
> work around or better solution?
>   

What does .libPaths() look like? I would guess you've got something like 
a relative path in there, which is probably a bad idea, for exactly the 
reason you're seeing.

Duncan Murdoch
> David
>
>
> On 08/07/2010 9:46 AM, David Bickel wrote:
>
> 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> <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"<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"<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"<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
>
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