R SIG Debian - Jan 2019 - [FORGED] r-base is already the newest version (3.5.2-1bionic)

Rolf,

I think it may help to read-up on dpkg and apt. Instead of 'whereis' do

  dpkg -l r-base-core

to see the content of that package.  Use

  apt-cache policy r-base-core

to see what the package cache says about where it gets the package from. And
so on.  Also

  type -p R
  which R

will tell where your system thinks R comes from. If you install R 3.5.2 you
should not see R 3.5.1.

These aren't really R issues. The package management system can be pure
source of joy. Something seems to have gotten crossed at your end but we
cannot tell what.

Dirk

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

On 1/30/19 11:53 AM, Dirk Eddelbuettel wrote:
> 
> Rolf,
> 
> I think it may help to read-up on dpkg and apt. Instead of
'whereis' do
> 
>    dpkg -l r-base-core
Now *that* was a revealing suggestion!  I did that and got:
> Desired=Unknown/Install/Remove/Purge/Hold
> |
Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
> ||/ Name             Version       Architecture  Description
>
+++-================-=============-=============-=====================================>
ii  r-base-core      3.5.2-1bionic amd64         GNU R core of statistical
computation
So indeed the installation had not actually been done.

The nature of the message prompted me to try

     sudo apt purge r-base-core

which ran and said that it was removing a whole lot of stuff.

I then tried

      sudo apt-get install r-base-core

which ran and gave a whole lot more output than was previously produced 
when I ran "sudo apt-get install r-base".  (Note: I had been typing
*r-base* and NOT *r-base-core*.)  It indicated that it was doing lots of 
stuff that looked promising in respect of actually *installing* R.

And in fact the promise was fulfilled.  I then started R and got:
> R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
> Copyright (C) 2018 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
Ta-da!!!

Was the problem essentially that I had been saying

"sudo apt-get install r-base" rather than

"sudo apt-get install r-base-core"?

Is it possible that the latter is needed if R has previously been 
installed from source, but otherwise just "r-base" is sufficient?

If so, it might be useful to note this in the instructions in

https://cran.r-project.org/bin/linux/ubuntu/README.html

<SNIP>

Anyhow, I now seem to be out of the woods, at long last.  Thanks for 
setting me on the path.

cheers,

Rolf

-- 
Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

On 30 January 2019 at 12:33, Rolf Turner wrote:
| On 1/30/19 11:53 AM, Dirk Eddelbuettel wrote:
| > 
| > Rolf,
| > 
| > I think it may help to read-up on dpkg and apt. Instead of
'whereis' do
| > 
| >    dpkg -l r-base-core

And I also meant  'dpkg -L r-base-core'.  Both -l and -L do useful (but
different) things.
 
| Now *that* was a revealing suggestion!  I did that and got:
| 
| > Desired=Unknown/Install/Remove/Purge/Hold
| > |
Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
| > |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
| > ||/ Name             Version       Architecture  Description
| >
+++-================-=============-=============-=====================================|
> ii  r-base-core      3.5.2-1bionic amd64         GNU R core of statistical
computation
| 
| So indeed the installation had not actually been done.

Why do you say that?  That is the __normal__ display after a successful
installation.
 
| The nature of the message prompted me to try
| 
|      sudo apt purge r-base-core
| 
| which ran and said that it was removing a whole lot of stuff.

Why?
 
| I then tried
| 
|       sudo apt-get install r-base-core
| 
| which ran and gave a whole lot more output than was previously produced 
| when I ran "sudo apt-get install r-base".  (Note: I had been typing
| *r-base* and NOT *r-base-core*.)  It indicated that it was doing lots of 
| stuff that looked promising in respect of actually *installing* R.
| 
| And in fact the promise was fulfilled.  I then started R and got:
| 
| > R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
| > Copyright (C) 2018 The R Foundation for Statistical Computing
| > Platform: x86_64-pc-linux-gnu (64-bit)
| 
| Ta-da!!!
| 
| Was the problem essentially that I had been saying
| 
| "sudo apt-get install r-base" rather than
| 
| "sudo apt-get install r-base-core"?

No. One is a superset. A meta package.

These are all __Debian__ or __Ubuntu__ questions.  Be patient, learn some
about your package manager.

And this is not the correct list for Debian or Ubuntu basics so it might be
polite of you to seek basic help elsewhere.

| Is it possible that the latter is needed if R has previously been 
| installed from source, but otherwise just "r-base" is sufficient?
| 
| If so, it might be useful to note this in the instructions in
| 
| https://cran.r-project.org/bin/linux/ubuntu/README.html
| 
| <SNIP>
| 
| Anyhow, I now seem to be out of the woods, at long last.  Thanks for 
| setting me on the path.

My pleasure. Glad you're set now.

Dirk

| 
| cheers,
| 
| Rolf
| 
| -- 
| Honorary Research Fellow
| Department of Statistics
| University of Auckland
| Phone: +64-9-373-7599 ext. 88276

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