Re: [R] package installation for Windows 7

Thu, 08 Jul 2010 06:56:59 -0700

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>  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

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