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issue with package updates

3 messages · Iryna Nikolayeva, Jim Lemon, Rolf Turner

Iryna Nikolayeva
# 
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:
[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:
_                           
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
Jim Lemon
# 
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:
Rolf Turner
# 
See below.
On 18/04/15 12:04, Jim Lemon wrote:

            

      
      
      
    

        
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