[R-SIG-Mac] Permission denied error while updating R packages
dwinsemius at comcast.net
Tue Mar 8 19:37:34 CET 2016
> 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:
>  "/Users/iryna/Library/R/3.1/library"
>  "/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:
> platform x86_64-apple-darwin13.4.0
> arch x86_64
> os darwin13.4.0
> system x86_64, darwin13.4.0
> 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:
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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