On Sun, 28 Apr 2013, Melissa Key wrote:
On Apr 28, 2013, at 2:15 AM, Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote:
a) You seem to be under the impression that running as Administrator
fixes problems... in my experience, it simply multiplies them. [1]
On a windows machine, I don't have any impressions either way. I find
the entire OS to be counter-intuitive and annoying, and I tend to take
the path of least resistance when it comes to playing with it. the
point I was trying to make was that it isn't an "insufficient
privileges" problem. I understand your point (and the point of the link
you sent), and I'll see how easy I find it to change the install folders
to a user folder. (right now, I do everything except installs in
Rstudio, so its pretty easy to open a instance of Rgui just for the
install.packages
Actually, the Administrator mode does not override all read and write
privilege settings in the filesystem... they are more complicated than
that. Truly, it is heroin you are dealing with.
b) Your personal library is in an unusual place... it is usually an R
directory under your Documents folder...
C:\Users\melissa\R\win-library\3.0
should normally be
C:\Users\melissa\Documents\R\win-library\3.0
on a Win7 system. This mis-location may be related to your problems.
This sounds like a potential culprit (along with c). I've been doing
standard R installs (nothing fancy, I promise), so I'm not sure why this
would be the case. Is there any easy way to correct this?
I don't know. It is possible that R is struggling with the hash you have
made of file permissions in your mucking with Administrator mode, and is
trying out default paths that used to work. Duncan may have more
constructive input here than I do.
You might want to look at R for Windows FAQ 2.17, or if you have any
environment variables that contain offensive paths.
Thanks for your response!
Melissa
c) Your errors seem to be suggesting that you have a Windows XP-style
personal library path in your install somewhere:
c:/Docume~1/melissa/R/win-library/3.0
That is definitely not kosher on a Win7 system.
[1] http://www.mail-archive.com/r-help@r-project.org/msg193966.html
On Sat, 27 Apr 2013, Melissa Key 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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/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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