Brian J. Knaus

Warning in install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl,  :
  'lib = "/usr/lib/R/site-library"' is not writable
Would you like to use a personal library instead?  (y/n) y
Would you like to create a personal library
NA
to install packages into?  (y/n) y
Error in install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl,  :
  unable to create ‘NA’

My system

First off its important to state that the system I’m discussing today is a work system on a work network, as opposed to a personal system. That means I need to avoid interrupting any network settings or else I’ll have to contact IT to get them to help me fix it. Fortunately, our netowrk is a Windows network, so I’m really more of an exception which may give me more flexibility than others.

My .libPaths()

As suggested by Dirk I checked the permissions of my /usr/local/lib/R/site-library.

$ ls -l /usr/local/lib/R/
total 4
drwxrwsr-x 2 root staff 4096 Aug  5  2016 site-library

Its owned by root and group memebership belongs to staff. I can check and see that I’m not a part of staff, which explains the error.

$ id
uid=1142428492(knausb) gid=1142424065(domain^users) groups=1142424065(domain^users),126(vboxusers),1142425304(grunwald-lab),1142428469(linux-users),1142429799(certsvc_dcom_access),1142429897(linux^admins)

Because I’m not actually the system administrator, I do not know a lot about the existing groups. I found this post which explains how I can query for the members of groups on my system. After creating the script I use the following to determine that there are no members of this group.

perl -T list_group_members.pl staff

This leads me to believe I can change it’s group ownership with no consequences.

$ sudo chgrp domain^users /usr/local/lib/R/site-library/
$ ls -l /usr/local/lib/R/
total 4
drwxrwsr-x 103 root domain^users 4096 Jul  6 10:16 site-library

Now I, and presumedly other users on this system if there are any, can install packages into /usr/local/lib/R/site-library/. Which means I have some package installations to work on.

Setting R_LIBS_USER

The above appears to be the ‘suggested’ manner to address this issue. However, there are options if the above does not suit you. For example, if you do not have administrator priviledges on the system you are working on, you will not be able to implement the above method. An alternate solution is to modify your Renviron file to set R_LIBS_USER. This can usually be found here:

/usr/lib/R/etc/Renviron

You should be able to locate the following lines.

# edd Jun 2017  Comment-out R_LIBS_USER
#R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/3.4'}
##R_LIBS_USER=${R_LIBS_USER-'~/Library/R/3.4/library'}

If you uncomment this so that it appears as follows,

# edd Jun 2017  Comment-out R_LIBS_USER
R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/3.4'}
##R_LIBS_USER=${R_LIBS_USER-'~/Library/R/3.4/library'}

and restart R, it should restore the behavior you are familiar with where a personal library is created at the indicated path. However, this still requires administrator privileges. If you add:

R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/3.4'}

to your ~/.Renviron file (where ‘~’ is your home directory). If you do not have this file already, you can create it. You should now gain behavior similar to the previous solution except that this should only affect your account as opposed to all system accounts. Happy package installing!