Dear R project members, I have an issue while automatically updating packages. For the packages installed in my second library, while automatically updating I get the following "Permission denied? messages(details below). I suppose I know where this problem comes from: I had installed a few different versions of R. And now I have 2 library paths:> .libPaths()[1] "/Users/iryna/Library/R/3.1/library" [2] "/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library? And for some reason R just doesn?t have rights to update packages in my second library. Do you know why is that? How should I fix this issue? Here is the error message: * installing *source* package ?mgcv? ... ** package ?mgcv? successfully unpacked and MD5 sums checked mv: rename /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv to /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/00LOCK-mgcv/mgcv: Permission denied Warning in file.copy(f, instdir, TRUE) : problem copying ./NAMESPACE to /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/NAMESPACE: Permission denied Warning in file(file, ifelse(append, "a", "w")) : cannot open file '/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/DESCRIPTION': Permission denied Error in file(file, ifelse(append, "a", "w")) : cannot open the connection ERROR: installing package DESCRIPTION failed for package ?mgcv? * removing ?/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv? Here are some additional information on my settings:> version_ platform x86_64-apple-darwin13.4.0 arch x86_64 os darwin13.4.0 system x86_64, darwin13.4.0 status major 3 minor 1.2 year 2014 month 10 day 31 svn rev 66913 language R version.string R version 3.1.2 (2014-10-31) nickname Pumpkin Helmet Thanks in advance for your help, ? Iryna Nikolayeva
Hi Iryna, The two paths seem to be a "user" path (one beneath your home directory) and a "system" path (one in another branch of the directory tree). You usually have to have superuser privileges to write files in the second. In most *NIX systems you use "su" to become "root" (the superuser), and if you can do this, then perform the update. Jim On Fri, Apr 17, 2015 at 7:25 PM, Iryna Nikolayeva <iryna.v.nikolayeva at gmail.com> wrote:> Dear R project members, > I have an issue while automatically updating packages. > For the packages installed in my second library, while automatically updating I get the following "Permission denied? messages(details below). > I suppose I know where this problem comes from: > I had installed a few different versions of R. > And now I have 2 library paths: >> .libPaths() > [1] "/Users/iryna/Library/R/3.1/library" > [2] "/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library? > > And for some reason R just doesn?t have rights to update packages in my second library. > Do you know why is that? How should I fix this issue? > > Here is the error message: > > * installing *source* package ?mgcv? ... > ** package ?mgcv? successfully unpacked and MD5 sums checked > mv: rename /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv to /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/00LOCK-mgcv/mgcv: Permission denied > Warning in file.copy(f, instdir, TRUE) : > problem copying ./NAMESPACE to /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/NAMESPACE: Permission denied > Warning in file(file, ifelse(append, "a", "w")) : > cannot open file '/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/DESCRIPTION': Permission denied > Error in file(file, ifelse(append, "a", "w")) : > cannot open the connection > ERROR: installing package DESCRIPTION failed for package ?mgcv? > * removing ?/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv? > > > > > Here are some additional information on my settings: >> version > _ > platform x86_64-apple-darwin13.4.0 > arch x86_64 > os darwin13.4.0 > system x86_64, darwin13.4.0 > status > major 3 > minor 1.2 > year 2014 > month 10 > day 31 > svn rev 66913 > language R > version.string R version 3.1.2 (2014-10-31) > nickname Pumpkin Helmet > > Thanks in advance for your help, > ? > > Iryna Nikolayeva > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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.
See below. On 18/04/15 12:04, Jim Lemon wrote:> Hi Iryna, > The two paths seem to be a "user" path (one beneath your home > directory) and a "system" path (one in another branch of the directory > tree). You usually have to have superuser privileges to write files in > the second. In most *NIX systems you use "su" to become "root" (the > superuser), and if you can do this, then perform the update.Jim: (1) The OP seems to be using a Mac OSX system (which has Unix underlying a great deal of gloppedy obfuscating point-and-click crap). (2) My reading of the help for install.packages() leads me to believe that by default the requested package should be installed into the *first* entry of .libPaths(), whence no superuser privileges should be required. It is mysterious to me why the system seems to be intent on using the *second* entry of .libPaths() so that superuser privileges *are* required. (3) Since this is Mac OSX stuff, the OP might get better mileage by posting on R-Sig-Mac. cheers, Rolf> > Jim > > On Fri, Apr 17, 2015 at 7:25 PM, Iryna Nikolayeva > <iryna.v.nikolayeva at gmail.com> wrote: >> Dear R project members, >> I have an issue while automatically updating packages. >> For the packages installed in my second library, while automatically updating I get the following "Permission denied? messages(details below). >> I suppose I know where this problem comes from: >> I had installed a few different versions of R. >> And now I have 2 library paths: >>> .libPaths() >> [1] "/Users/iryna/Library/R/3.1/library" >> [2] "/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library? >> >> And for some reason R just doesn?t have rights to update packages in my second library. >> Do you know why is that? How should I fix this issue? >> >> Here is the error message: >> >> * installing *source* package ?mgcv? ... >> ** package ?mgcv? successfully unpacked and MD5 sums checked >> mv: rename /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv to /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/00LOCK-mgcv/mgcv: Permission denied >> Warning in file.copy(f, instdir, TRUE) : >> problem copying ./NAMESPACE to /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/NAMESPACE: Permission denied >> Warning in file(file, ifelse(append, "a", "w")) : >> cannot open file '/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/DESCRIPTION': Permission denied >> Error in file(file, ifelse(append, "a", "w")) : >> cannot open the connection >> ERROR: installing package DESCRIPTION failed for package ?mgcv? >> * removing ?/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv? >> >> >> >> >> Here are some additional information on my settings: >>> version >> _ >> platform x86_64-apple-darwin13.4.0 >> arch x86_64 >> os darwin13.4.0 >> system x86_64, darwin13.4.0 >> status >> major 3 >> minor 1.2 >> year 2014 >> month 10 >> day 31 >> svn rev 66913 >> language R >> version.string R version 3.1.2 (2014-10-31) >> nickname Pumpkin Helmet >> >> Thanks in advance for your help, >> ? >> >> Iryna Nikolayeva-- Rolf Turner Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 Home phone: +64-9-480-4619