On Feb 23, 2016, at 11:11 AM, Iryna Nikolayeva <iryna.v.nikolayeva at 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
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