[R] path reference problems in R 3.0.0

[Gabor Grothendieck]

On Sat, Apr 27, 2013 at 3:08 PM, Melissa Key <mkcheste at mac.com> wrote:
> Hi-
>
>
>
> I just upgraded R to 3.0.0 from 2.15.1 (which worked fine).  When I started
> trying to install updated versions of the libraries, I saw the following
> error:
>
>
>
>> install.packages("lme4")
>
> Installing package into 'c:/Docume~1/melissa/R/win-library/3.0'
>
> (as 'lib' is unspecified)
>
> Warning in install.packages :
>
>   path[1]="c:/Docume~1/melissa/R/win-library/3.0": Access is denied
>
> trying URL
> 'http://cran.case.edu/bin/windows/contrib/3.0/lme4_0.999999-2.zip'
>
> Content type 'application/zip' length 1408286 bytes (1.3 Mb)
>
> opened URL
>
> downloaded 1.3 Mb
>
>
>
> Error in install.packages : path[1]="c:\Docume~1\melissa\R\win-library\3.0":
> Access is denied
>
>
>
> At that point, I noticed that a similar error was occurring when R loads:
>
> Warning message:
> In normalizePath(path.expand(path), winslash, mustWork) :
>   path[1]="c:/Docume~1/melissa/R/win-library/3.0": Access is denied
>
>
>
> The relevant directory does exist, although it keeps getting set to
> "read-only".  I can't imagine that being a big issue if I'm running R as an
> administrator though
>
> C:\Users\melissa\R\win-library\3.0
>
>
>
> Also, I can successfully install packages into other directories (e.g. when
> running as an administrator, this works fine):
>
>> install.packages("lme4", lib="C:/Program Files/R/R-3.0.0/library")
> trying URL
> 'http://cran.case.edu/bin/windows/contrib/3.0/lme4_0.999999-2.zip'
> Content type 'application/zip' length 1408286 bytes (1.3 Mb)
> opened URL
> downloaded 1.3 Mb
>
> package 'lme4' successfully unpacked and MD5 sums checked
>
> The downloaded binary packages are in
>         C:\Users\melissa\AppData\Local\Temp\RtmpEXtf89\downloaded_packages
>
>
>
> This will allow me to work with most R packages, but not Bioconductor, due
> path to the references in the biocLite source file.
>
>
>
> I haven't seen any other messages regarding similar issues, so I'm not sure
> what is going on.  I've tried reinstalling R, (although I didn't try a fresh
> download).
>
>
>
> Other relevant details:
>
> This is a personal computer running windows 7.
>
>
>
>
>
> Any thoughts or ideas of how to get this to work?
>

1. Grab the batchfiles distribution:
   http://batchfiles.googlecode.com
and place R.bat on your Windows PATH; then at the Windows cmd line enter
   R.bat gui
and see if that works.  (See batchfiles.pdf for more info.)

2. If that works you are done but if that does not work then suitably
set the paths by hand in Rpathset.bat (the example settings should
give you the idea) and from the Windows cmd line enter:

   Rpathset.bat
   Rgui.exe