[R] issue with package updates

[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:
> 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:
>> .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
> 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
>
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