R SIG Debian - Nov 2018 - Problem Upgrading to R 3.5 on Ubuntu 18.04

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).

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?

Thanks,
Liz

-- 
Elizabeth Tighe, Ph.D.
Research Scientist
Steinhardt Social Research Institute
Brandeis University
781.736.3824

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 at debian.org

Thanks Dirk!? The prior install and updates had been running fine for so 
long I forgot all about the documentation on Renviron, Startup, etc.!? 
Thanks.? Will changing the libPaths in Renviron.site help with the issue 
that the operating system doesn't seem to recognize the installation re: 
message that the "software is not installed" when I tried to remove
it??
Also what does it mean in your note when you say: "you will need to 
trace want on your box does"?

Thanks!

Liz

On 11/28/2018 1:12 PM, Dirk Eddelbuettel wrote:
> 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
>
-- 
Elizabeth Tighe, Ph.D.
Research Scientist
Steinhardt Social Research Institute
Brandeis University
781.736.3824