[R-sig-Debian] Outdated r-base-core when installing on Ubuntu 14.04

Dirk Eddelbuettel edd at debian.org
Mon Mar 21 18:59:47 CET 2016 

On 21 March 2016 at 12:35, Dirk Eddelbuettel wrote:
| 
| On 21 March 2016 at 12:10, Matthew Simpson wrote:
| | I have a chromebook with a fresh minimal install of Ubuntu 14.04 running
| | through crouton, and I'm trying to install the latest version of R. The
| | only thing I have done to the system before trying to install R is install
| | gedit. When I try to install R I get an unmet dependencies error that
| | complains that the version of r-base-core available isn't new enough.
| | 
| | I followed the instructions at
| | https://cran.r-project.org/bin/linux/ubuntu/README.html to install R. Here
| | is precisely what I did:
| | 
| | 1) after installing gedit, I added the following two lines to
| | /etc/apt/sources.list
| | 
| | deb http://cran.wustl.edu/bin/linux/ubuntu trusty/
| | deb http://ports.ubuntu.com/ubuntu-ports/ trusty-backports main restricted
| | universe
| | 
| | (Note: I've tried a couple different R mirrors and it doesn't affect
| | anything as far as I can
| | tell)
| | 
| | 2) Add Michael Rutter's key with
| | 
| | sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
| | 
| | 3) Update sources and attempt to install R:
| | 
| | sudo apt-get update
| | sudo apt-get install r-base
| | 
| | Here is the full text of the error I get:
| | 
| | sudo apt-get install r-base
| | Reading package lists... Done
| | Building dependency tree
| | Reading state information... Done
| | Some packages could not be installed. This may mean that you have
| | requested an impossible situation or if you are using the unstable
| | distribution that some required packages have not yet been created
| | or been moved out of Incoming.
| | The following information may help to resolve the situation:
| | 
| | The following packages have unmet dependencies:
| |  r-base : Depends: r-base-core (>= 3.2.4-revised-1trusty0) but it is not
| | going to be installed
| |           Depends: r-recommended (= 3.2.4-revised-1trusty0) but it is not
| | going to be installed
| |           Recommends: r-base-html but it is not going to be installed
| |           Recommends: r-doc-html but it is not going to be installed
| | E: Unable to correct problems, you have held broken packages.
| | 
| | 
| | Using sudo apt-cache showpkg <package> reveals that apt is attempting to
| | install r-base 3.2.4, but only has access to r-base-core 3.0.2.  It does
| | have access to r-recommended, r-base-html, and r-doc-html all version 3.2.4
| | though.
| 
| Then something is wrong with your apt entries. Check and double check.
| 
| I run wily here (because why would I want to be on an almost two year old
| OS?) and it looks as follows:
| 
| edd at max:~$ apt-cache policy r-base
| r-base:
|   Installed: (none)
|   Candidate: 3.2.4-revised-1wily0
|   Version table:
|      3.2.4-revised-1wily0 0
|         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
|      3.2.4-1wily 0
|         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
|      3.2.3-6wily0 0
|         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
|      3.2.3-4wily0 0
|         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
|      3.2.3-3wily0 0
|         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
|      3.2.3-1.wily.0 0
|         500 http://ppa.launchpad.net/edd/misc/ubuntu/ wily/main amd64 Packages
|      3.2.3-1wily1 0
|         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
|      3.2.3-1wily0 0
|         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
|      3.2.2-1wily 0
|         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
|      3.2.2-1 0
|         500 http://archive.ubuntu.com/ubuntu/ wily/universe amd64 Packages
| edd at max:~$ 
| 
| I could have 3.2.2 from the distro -- which makes sense as 15.10 had a cutoff
| some time last summer -- all the other thanks to Michael rebuilding the ports
| of why I stick into Debian.

Sorry for the sloppy writing. One day I will remember to proof-read.

Here is another example, using the rocker image r-apt for trusty:

edd at max:~$ docker run --rm -ti rocker/r-apt:trusty apt-cache policy r-base
r-base:
  Installed: 3.2.3-1trusty0
  Candidate: 3.2.3-1trusty0
  Version table:
 *** 3.2.3-1trusty0 0
        500 http://ppa.launchpad.net/marutter/rrutter/ubuntu/ trusty/main amd64 Packages
        100 /var/lib/dpkg/status
     3.0.2-1ubuntu1 0
        500 http://archive.ubuntu.com/ubuntu/ trusty/universe amd64 Packages
edd at max:~$

I haven't updated my local copy of the container so it still points to
3.2.3.  But at least you can see _all steps undertaken to get the container_
in this file:

https://github.com/rocker-org/rocker/blob/master/r-apt/trusty/Dockerfile

It uses Michael's two PPAs directly and doesn't even point at the CRAN
mirror.  You can just copy and paste the commands ...

Dirk

| 
| Dirk
| 
| | 
| | I could probably live with R 3.0.2, but sudo apt-get install r-base=3.0.2
| | yields a similar error complaining that it needs r-recommended 3.0.2, but
| | it won't be installed.
| | 
| | Any help would be appreciated.
| | 
| | Thanks,
| | Matt Simpson
| | 
| | 	[[alternative HTML version deleted]]
| | 
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| 
| -- 
| http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
| 
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