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> 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@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. > -- 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.m...@ugent.be ------------------------------- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php ______________________________________________ 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.