 Now that I have installed R outside "Program files" to get past the
permissions problem, there are packages I can only access from certain
working directories:

> setwd("U:/Calc/zTemp") # "U:" points to a USB hard drive
> library(splines) # ok
> library(locfdr)
Error in library(locfdr) : there is no package called 'locfdr'
> setwd("C:/Users/dbickel/Documents")
> library(locfdr) # ok

The same error occurs whether or not I run R as administrator. Is there a
work around or better solution?

David


On 08/07/2010 9:46 AM, David Bickel wrote:

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+reply@gmail.com> <davidbickel.com+reply@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"<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"<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"<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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