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? 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+re...@gmail.com> <davidbickel.com+re...@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@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@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.