[R] path reference problems in R 3.0.0

[annoporci]

When I encounter these problems, I usually fix them with the following:

1. take ownership of the directories where the libraries are stored,
here's how I do it on windows:

http://www.howtogeek.com/howto/windows-vista/add-take-ownership-to-explorer-right-click-menu-in-vista/


2. have an Renviron file store the user's default library path (I store my  
library in "C:/R/library"), here's how I do it:

Create an environment file named .Renviron place it in the working  
directory or home directory:

"C:/Users/username/Documents"

Query the paths to check that your system is reading the Renviron.site  
file.

Some users have reported that the .Renviron file needed to be in  
"c:/users/username" instead.

If you're not sure where to place it, save the desktop history and see  
where the .Rhistory file is located. Then place your .Renviron file in the  
same location. To save history savehistory()

# Windows .Renviron file:
R_LIBS_USER = "C:/R/library"
R_USER = "C:/R"
R_DOC_DIR = "C:/R"
HOME = "C:"



3. make sure that the directories are in the system's PATH

# Set global PATH on Windows

My Computer / Properties / Advanced System Settings / Environment  
Variables --> user variables --> Path --> Edit c:\R;c:\R\library;



This is what has worked for me, I hope some of it helps.



On Sun, 28 Apr 2013 03:08:05 +0800, 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?
>
>
> Thank you!
>
>
> Melissa Key
>
>
>
> 	[[alternative HTML version deleted]]
>
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-- 
Patrick Toche.