> On Feb 23, 2016, at 11:11 AM, Iryna Nikolayeva <iryna.v.nikolay...@gmail.com> > wrote: > > Dear R-Sog-Mac members, > > I have an issue while automatically updating packages in R. > 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”
This is just a guess, ... did you install that version of R through MacPorts? The most recent version of OSX has nailed down a lot of system folders to which write access used to be available. > > 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) You should use the binary installer package to update to the current version of R. Then your .libPaths() result should be: [1] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library" You can then add "/Users/iryna/Library/R/3.2/library" with: .libPaths(c("/Users/iryna/Library/R/3.2/library", .libPaths() ) ) , then copy old packages from your libraries, and run (from the R console): update.packages(checkBuilt=TRUE) > > nickname Pumpkin Helmet > > Thanks in advance for your help, > Iryna Nikolayeva > > [[alternative HTML version deleted]] Please post in plain text. > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac David Winsemius Alameda, CA, USA _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac