[R] path reference problems in R 3.0.0

[Melissa Key]

On Apr 28, 2013, at 2:15 AM, Jeff Newmiller <jdnewmil at 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


> 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?  

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
>> 
>> 
>> 
>> 
>> 	[[alternative HTML version deleted]]
>> 
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>> 
> 
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