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
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. >-- 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.Meys at Ugent.be ------------------------------- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
On 08/07/2010 7:15 AM, Dave Bickel wrote:> Neither biocLite nor the GUI menus can install packages on my system. >This is probably a permissions problem. Are you running R as an administrator when you try the install? If not, you won't be able to install to the default location, but you should be able to set up your own library somewhere else, and install there. The error message should be fixed; we shouldn't give Error in if (ok) { : missing value where TRUE/FALSE needed but I doubt if that's the source of your problem. BTW, in future Bioconductor questions should go to their list. In this case it looks as though it's not a BioC problem, but that just means there's no need to list all the biocLite.R material at the start: short simple bug reports are easier to deal with. Duncan Murdoch> 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 > >