[R] package installation for Windows 7

[Joris Meys]

As far as my experience goes, there is no need whatsoever to run R as
an administrator for installation of any package, including
BioConductor, provided you stay away from the "Program Files" folder.

Cheers
Joris

On Thu, Jul 8, 2010 at 2:55 PM, Duncan Murdoch <murdoch.duncan at gmail.com> 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
>>
>>
>
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>



-- 
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
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