[R-sig-Debian] Problem Upgrading to R 3.5 on Ubuntu 18.04

[Dirk Eddelbuettel]

On 28 November 2018 at 12:37, Elizabeth Tighe wrote:
| Somehow during the process of updating both Ubuntu and R to the latest 
| versions I ended up with a version of R 3.5 installed into the sudo 
| user's home directory with default libraries set to the sudo user home 
| directory as well (/home/uname/R/x86_64-pc-linux-gnu-library/3.5 rather 
| than usr/local/lib/R/site-library).

"Hate when that happens" :)
 
| I've tried to remove using sudo apt purge r-base r-base-dev and get a 
| message that the software is not installed. If I type "R" it opens 
| version 3.5.  If I go to Ubuntu's graphical interface as sudo user, 
| Software library, R is listed as installed and if I click on the 
| "Remove" button, nothing happens ...
| 
| Any suggestions on how to expunge this rogue installation and start anew?

What you had (and what you want, if I read the message correctly) is an
explicit setting for (e.g.) .libPaths() which I like, but which I can't
"enforce" in the package -- I once tried about 1 1/2 years ago and all broke
loose because those who had ~/R/... path no longer saw it.

So now again, and as it had been since the 2000s, this is governed by a
setting in eg

  /etc/R/Renviron.site

which is a convenience symbolic link to

  /usr/lib/R/etc/Renviron.site

The file has comments, so see those.  My (personal) version just comments the
settings out so that I get

  R> .libPaths()
  [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"       "/usr/lib/R/library"           
  R> 

Now, the tricky bit that R allows half a dozen ways to influence this -- see
help(Startup) in R for all the gory details.  So I fiddling with
Renviron.site does not influence a fresh R session you will need to trace
want on your box does -- "dotfiles" can be sourced from the current
directory, the home directory, the /etc/ directory, ... and environment
variables enter too.

Keep us posted, hope this gets you started.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org