[R] package installation for Windows 7

[Duncan Murdoch]

On 10/07/2010 10:37 AM, David Bickel wrote:
> Thank you, Prof. Murdoch. I have this:
>
>  > .libPaths()
> [1] "\\Users\\dbickel/R/win-library/2.11" "C:/R/R-2.11.1/library"
>   

That first path doesn't look like it would work in Windows:  it has no 
drive letter, so its meaning will depend on the driver letter of the 
current working directory.  Effectively it's a relative path.

Duncan Murdoch
> Since the following naive line in the profile failed, I just moved the 
> new packages to the same directory as the default packages.
>
> .libPaths(c("C:/Users/dbickel/R/win-library/2.11/", .libPaths()))
>
> Best regards,
> David
>
>
> On 10/07/2010 8:43 AM, Duncan Murdoch wrote:
>   
>> David Bickel wrote:
>>     
>>>  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?
>>>       
>> What does .libPaths() look like? I would guess you've got something 
>> like a relative path in there, which is probably a bad idea, for 
>> exactly the reason you're seeing.
>>
>> Duncan Murdoch
>>     
>>> 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 at gmail.com> <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"<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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>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
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>>>
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
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>>>
>>>   
>>> ------------------------------------------------------------------------
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
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>>> PLEASE do read the posting guide 
>>> http://www.R-project.org/posting-guide.html
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>>>       
>
>