R SIG Debian - Mar 2016 - Outdated r-base-core when installing on Ubuntu 14.04

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.

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]]

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.

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]]
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

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

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]]
| | 
| | _______________________________________________
| | R-SIG-Debian mailing list
| | R-SIG-Debian at r-project.org
| | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| 
| -- 
| http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

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

Since 14.04 is the Long Term Support version, which also is used by
Linux Mint, it's not really outdated, and a lot of folk, myself
included, use that stream (my machine says Linux Mint 17.1, but I think
that is simply the splash screen). I say stream, because the kernel and
other infrastructure are  being updated, though probably not to the
level Dirk prefers, and I do use other distros for some work. My own
sources.list includes

deb http://cran.stat.sfu.ca/bin/linux/ubuntu trusty/

and R updated fine to 3.2.4 last week with a typical automated prompt
that there were updates available.

So maybe Matt's problem is something else. This was the first time I'd
read about crouton (I run regular Linux distros). Is that getting in the
way somehow?

JN



On 16-03-21 01:35 PM, 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.
> 
> 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]]
> | 
> | _______________________________________________
> | R-SIG-Debian mailing list
> | R-SIG-Debian at r-project.org
> | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>