R SIG Debian - Jan 2018 - lost ability to apt-get install r-base=3.4.2-1trusty1

Hello,

I need a specific version of R installed for consistency reasons. I do the
standard setup steps:

echo "deb https://cran.ma.imperial.ac.uk/bin/linux/ubuntu trusty/" |
sudo tee -a /etc/apt/sources.list
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo apt-get update

And then a simple install call, which used to work just fine some time ago,
tosses an error:

ubuntu at test:~$ sudo apt-get -y install r-base=3.4.2-1trusty1
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-recommended (= 3.4.2-1trusty1) but 3.4.3-1trusty0 is 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.

The problem is highlighted in this error - r-recommended seems to auto-default
to 3.4.3. When installing r-base-core=3.4.2-1trusty1 by itself, it installs
fine. When installing r-recommended=3.4.2-1trusty1 by itself, it sneakily
installs 3.4.3 without saying anything. When trying to install
r-base=3.4.2-1trusty1, it catches this cognitive dissonance and falls on its
face. Some help please?

Sincerely,
Krzysztof



-- 
 The Wellcome Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 



	[[alternative HTML version deleted]]

Dear Krzysztof,

I would suggest to have a look at Docker images.
https://hub.docker.com/r/rocker/r-ver/ provides images for different
versions of R. You could even create your own image with all the
packages and other dependencies that you need. See e.g. our image at
https://hub.docker.com/r/inbobmk/rstable/

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx at inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

///////////////////////////////////////////////////////////////////////////////////////////
To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data. ~ John Tukey
///////////////////////////////////////////////////////////////////////////////////////////




2018-01-16 19:32 GMT+01:00 Krzysztof Polanski <kp9 at
sanger.ac.uk>:
> Hello,
>
> I need a specific version of R installed for consistency reasons. I do the
standard setup steps:
>
> echo "deb https://cran.ma.imperial.ac.uk/bin/linux/ubuntu
trusty/" | sudo tee -a /etc/apt/sources.list
> sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
> sudo apt-get update
>
> And then a simple install call, which used to work just fine some time ago,
tosses an error:
>
> ubuntu at test:~$ sudo apt-get -y install r-base=3.4.2-1trusty1
> 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-recommended (= 3.4.2-1trusty1) but 3.4.3-1trusty0 is
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.
>
> The problem is highlighted in this error - r-recommended seems to
auto-default to 3.4.3. When installing r-base-core=3.4.2-1trusty1 by itself, it
installs fine. When installing r-recommended=3.4.2-1trusty1 by itself, it
sneakily installs 3.4.3 without saying anything. When trying to install
r-base=3.4.2-1trusty1, it catches this cognitive dissonance and falls on its
face. Some help please?
>
> Sincerely,
> Krzysztof
>
>
>
> --
>  The Wellcome Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>
>
>
>         [[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

On 17 January 2018 at 09:42, Thierry Onkelinx wrote:
| Dear Krzysztof,
| 
| I would suggest to have a look at Docker images.
| https://hub.docker.com/r/rocker/r-ver/ provides images for different
| versions of R.

Indeed!  And see eg our forthcoming / in-print R Journal paper with some
details, background, motivation, ... on both Rocker and "versioned"
images:

   https://rjournal.github.io/archive/2017/RJ-2017-065/index.html
   
| You could even create your own image with all the
| packages and other dependencies that you need. See e.g. our image at
| https://hub.docker.com/r/inbobmk/rstable/

Yep. Ubuntu simply cannot offer you the ability to get _any odd version_ of
your choosing at any odd time.  Debian, with its volunteers, has something
like that in the "Snapshot" repository at

   http://snapshot.debian.org/

but Debian also cuts releases differently.

Dirk

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