path reference problems in R 3.0.0
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