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 <mkche...@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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
