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]]
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
a) You seem to be under the impression that running as Administrator fixes problems... in my experience, it simply multiplies them. [1] 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. 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 at 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
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 <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? > > > 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.-- Patrick Toche.
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