[R] Cannot install packages in R 2.12.0 on Windows 7

[Dick Beyer]

Thanks very much for your help.  This was a case of some weird network card IP reset hardware error that did something to permissions or something during the install.  Not exactly sure if this was part of the problem.  But getting the hardware corrected and reinstalling R 2.12.0 solved the problem.  I'm filing this under really obscure errors.

Cheers,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/members_fc_bioinfo.html
http://staff.washington.edu/~dbeyer
*******************************************************************************

On Tue, 16 Nov 2010, Prof Brian Ripley wrote:

> The error seems to be a BioC problem[*] and associated with having a package 
> installed with an empty DESCRIPTION file.  So please take a look at your 
> installed packages and remove any such.
>
> The following R code may help:
>
> for(lib in .libPaths()) {
>    descs <- Sys.glob(file.path(lib, "*", "DESCRIPTION"))
>    sizes <- file.info(descs)$size
>    names(sizes) <- descs
>    print(sizes[sizes < 100])
> }
>
> [*] They don't know how they did it, but reported this symptom on R-devel 
> recently.
>
> On Mon, 15 Nov 2010, Dick Beyer wrote:
>
>> Hi,
>> 
>> I am unable to install packages on my R 2.12.0 Windows 7 machine. Here are 
>> the relevant lines:
>> 
>> sessionInfo()
>> R version 2.12.0 (2010-10-15)
>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>> 
>> locale:
>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United 
>> States.1252    LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C                           LC_TIME=English_United 
>> States.1252
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>>> source("http://www.bioconductor.org/biocLite.R")
>> BioC_mirror = http://www.bioconductor.org
>> Change using chooseBioCmirror().
>>> biocLite("Biobase")
>> Using R version 2.12.0, biocinstall version 2.7.4.
>> Installing Bioconductor version 2.7 packages:
>> [1] "Biobase"
>> Please wait...
>> 
>> Error: subscript out of bounds
>> 
>>> traceback()
>> 7: .readPkgDesc(lib, fields)
>> 6: installed.packages(lib.loc = libpath, fields = c("Package", "Version"))
>> 5: getDependencies(pkgs, dependencies, available, lib)
>> 4: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
>>       method = method, available = available, destdir = destdir,
>>       dependencies = dependencies, libs_only = libs_only, ...)
>> 3: install.packages(pkgs = pkgs, repos = repos, ...) at biocinstall.R#205
>> 2: biocinstall(pkgs = pkgs, groupName = groupName, ...) at biocLite.R#5
>> 1: biocLite("Biobase")
>> 
>> 
>> It doesn't matter if I use biocLite, or just install.packages(), I get the 
>> same error. I did a re-install of R, but that didn't help.  I'm hoping 
>> someone else has seen this error and might have a suggestion.
>> 
>> Thanks very much,
>> Dick
>> *******************************************************************************
>> Richard P. Beyer, Ph.D.	University of Washington
>> Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
>> Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
>> 			Seattle, WA 98105-6099
>> http://depts.washington.edu/ceeh/members_fc_bioinfo.html
>> http://staff.washington.edu/~dbeyer
>
>
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>