[R] path reference problems in R 3.0.0
Jan van der Laan
rhelp at eoos.dds.nl
Sun Apr 28 09:18:03 CEST 2013
Some colleagues ran into similar problems after migrating to windows 7.
They could no longer install packages in certain network locations
because the read only bit was set (which could be unset after which
windows set it again). Perhaps the following helps:
http://itexpertvoice.com/home/fixing-the-windows-7-read-only-folder-blues/
Jan
On 04/28/2013 08:43 AM, Jeff Newmiller wrote:
> On Sun, 28 Apr 2013, Melissa Key wrote:
>
>>
>> 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
>
> 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
>>>>
>>>>
>>>>
>>>>
>>>> [[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.
>>>>
>>>
>>> ---------------------------------------------------------------------------
>>>
>>> Jeff Newmiller The ..... ..... Go
>>> Live...
>>> DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live
>>> Go...
>>> Live: OO#.. Dead: OO#.. Playing
>>> Research Engineer (Solar/Batteries O.O#. #.O#. with
>>> /Software/Embedded Controllers) .OO#. .OO#.
>>> rocks...1k
>>> ---------------------------------------------------------------------------
>>>
>>
>
> ---------------------------------------------------------------------------
> Jeff Newmiller The ..... ..... Go Live...
> DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go...
> Live: OO#.. Dead: OO#.. Playing
> Research Engineer (Solar/Batteries O.O#. #.O#. with
> /Software/Embedded Controllers) .OO#. .OO#. rocks...1k
>
> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide
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