[R] package installation for Windows 7

Sat Jul 10 16:37:54 CEST 2010

Thank you, Prof. Murdoch. I have this:

 > .libPaths()
[1] "\\Users\\dbickel/R/win-library/2.11" "C:/R/R-2.11.1/library"

Since the following naive line in the profile failed, I just moved the 
new packages to the same directory as the default packages.

.libPaths(c("C:/Users/dbickel/R/win-library/2.11/", .libPaths()))

Best regards,
David

On 10/07/2010 8:43 AM, Duncan Murdoch wrote:
> 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
>>
>> ______________________________________________
>> 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<http://www.r-project.org/posting-guide.html> 
>>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>     [[alternative HTML version deleted]]
>>
>>   
>> ------------------------------------------------------------------------
>>
>> ______________________________________________
>> 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.
>

-- 
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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