R SIG Debian - Jan 2015 - Unable to install R 3.1.2 on Debian:Testing

Dear Johannes, R-sig-debian list,

Along with Dirk Eddelbuettel I've been maintaining Debian-based Docker
containers for R. Recently our container installing r-base has started to
fail. This seems to be due to a problem with the libjpeg dependencies. The
example I show below was working with debian:jessie on Jan 5th, but has
been failing since then.  (https://registry.hub.docker.com/u/rocker/r-base/
)
>From a vanilla install of debian:testing (or jessie or squeeze) I add the
CRAN repository for the latest R version for debian, and then I then try to
install `r-base-core` 3.1.2:

    apt-key adv --keyserver keys.gnupg.net --recv-key 381BA480
    echo "deb http://cran.rstudio.com/bin/linux/debian wheezy-cran3/"
>
/etc/apt/sources.list.d/r-cran.list

    apt-get install r-base-core=3.1.2*

and I get the error:








*Selected version '3.1.2-1~wheezycran3.0' (CRAN Backports:wheezy-cran3
[amd64]) for 'r-base-core'Some packages could not be installed. This may
mean that you haverequested an impossible situation or if you are using the
unstabledistribution that some required packages have not yet been
createdor been moved out of Incoming.The following information may help to
resolve the situation:*

*The following packages have unmet dependencies: r-base-core : Depends:
libjpeg8 (>= 8c) but it is not installable*


Note that `apt-cache show r-base-core` shows three versions are available:
3.1.2~wheezycran3.0, 3.1.1+b2, and 3.1.0~wheezycran3.0, and that the
`wheezycran3.0` versions (e.g. R 3.1.2 and 3.1.0) cannot be installed
because they depend on libjpeg8, which is not available, while 3.1.1
depends on libjpeg62-turbo-dev.

I'm not sure why the libjpeg dependency has changed or how to address this
so that I can install r-base=3.1.2 on Debian.


Thanks for your help,

Carl

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Dear Carl,

the CRAN repository does not support Debian testing. I did think of adding
support for jessie,
as it is frozen now, but did not get around to do it yet.

I believe you would have no problem when using Debian stable.

Am Freitag, 16. Januar 2015, 21:44:25 schrieb Carl
Boettiger:
> Dear Johannes, R-sig-debian list,
> 
> Along with Dirk Eddelbuettel I've been maintaining Debian-based Docker
> containers for R. Recently our container installing r-base has started to
> fail. This seems to be due to a problem with the libjpeg dependencies. The
> example I show below was working with debian:jessie on Jan 5th, but has
> been failing since then.  (https://registry.hub.docker.com/u/rocker/r-base/
> )
> 
> From a vanilla install of debian:testing (or jessie or squeeze) I add the
Well, testing and jessie are the same. For squeeze you would have to add
squeezecran
sources.
> CRAN repository for the latest R version for debian, and then I then try to
> install `r-base-core` 3.1.2:
 
...
...
> Note that `apt-cache show r-base-core` shows three versions are available:
I should clean this up - generally I only have the latest released version in
the repository.
> 3.1.2~wheezycran3.0, 3.1.1+b2, and 3.1.0~wheezycran3.0, and that the
> `wheezycran3.0` versions (e.g. R 3.1.2 and 3.1.0) cannot be installed
> because they depend on libjpeg8, which is not available, while 3.1.1
> depends on libjpeg62-turbo-dev.
> 
> I'm not sure why the libjpeg dependency has changed or how to address
this
> so that I can install r-base=3.1.2 on Debian.
At the moment you are on your own with R 3.1.2 on jessie. The easiest safe bet
in my opinion
would be to install from the Debian sources in unstable, i.e. add a deb-src
entry for unstable
to your sources.list, do an apt-get build-dep r-base and then apt-get source
--build r-base
and install the packages with dpkg.
> Thanks for your help,
> 
> Carl
Hope it helps.

Johannes



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Hi Johannes,

On 18 January 2015 at 20:47, Johannes Ranke wrote:
| At the moment you are on your own with R 3.1.2 on jessie. The easiest safe bet
in my opinion
| would be to install from the Debian sources in unstable, i.e. add a deb-src
entry for unstable
| to your sources.list, do an apt-get build-dep r-base and then apt-get source
--build r-base
| and install the packages with dpkg.

Ok. I will set up a new toolchain for testing then. We need this for Rocker
all the time---eg I just put something marvelous into littler which I need in
Rocker, yet Debian is frozen with no timeline for release. And it is silly
for us to keep rebuilding all these things when building containers.

The three of us should (will !!) work something out that will allow us proper
testing support via CRAN, which we can fold into your existing mirror
structure.  Plan?

Cheers, Dirk

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