[R] package installation for Windows 7

[David Bickel]

Yes, the User into which I logged in before launching RGui is an 
Administrator. Correct, the problem is not limited to Bioconductor packages.

David


On 08/07/2010 8:55 AM, Duncan Murdoch wrote:
> 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
>>
>


-- 
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
dbickel at uottawa.ca

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