[R-SIG-Mac] Permission denied error while updating R packages

Iryna Nikolayeva iryna.v.nikolayeva at gmail.com
Tue Feb 23 20:11:06 CET 2016

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” 

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        
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 

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