R SIG Debian - May 2022 - Installing R 4.1.2 doesn't work as it did a week ago

It looks like there are even more unmet dependencies on Ubuntu 20.04:

#9 1.337 The following packages have unmet dependencies:
#9 1.415  r-recommended : Depends: r-cran-cluster (>= 1.9.6-2) but it is
not going to be installed
#9 1.415                  Depends: r-cran-lattice (>= 0.10.11) but it is
not going to be installed
#9 1.415                  Depends: r-cran-mgcv (>= 1.1.5) but it is not
going to be installed
#9 1.415                  Depends: r-cran-nlme (>= 3.1.52) but it is not
going to be installed
#9 1.415                  Depends: r-cran-rpart (>= 3.1.20) but it is not
going to be installed
#9 1.415                  Depends: r-cran-survival (>= 2.13.2-1) but it is
not going to be installed
#9 1.415                  Depends: r-cran-mass but it is not going to be
installed
#9 1.415                  Depends: r-cran-class but it is not going to be
installed
#9 1.415                  Depends: r-cran-matrix but it is not going to be
installed

Using the commands

RUN apt-get install --yes  \
    r-base=4.1.2-* \
    r-base-dev=4.1.2-* \
    r-base-core=4.1.2-* \
    r-recommended=4.1.2-*

I can explicitly install each of the dependent packages, but it feels
excessive. Any ideas why this is the case? Below is a Dockerfile that
reproduces the dependencies messages.


FROM ubuntu:20.04

RUN apt-get update \
  && apt-get install --yes \
    bash \
    sudo \
    coreutils \
    procps

ENV DEBIAN_FRONTEND=noninteractive

RUN apt-get update \
  && apt-get install --yes software-properties-common
apt-transport-https \
  && gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys
E298A3A825C0D65DFD57CBB651716619E084DAB9 \
  && gpg -a --export E298A3A825C0D65DFD57CBB651716619E084DAB9 | sudo
apt-key add - \
  && add-apt-repository -y "deb [arch=amd64,i386]
https://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -cs)-cran40/" \
  && apt-get update \
  && apt-get install --yes \
    libssl-dev \
    r-base=4.1.2-* \
    r-base-dev=4.1.2-* \
    r-base-core=4.1.2-* \
    r-recommended=4.1.2-*

Chad Young
Bioinformatics Scientist
TwinStrand Biosciences <https://twinstrandbio.com/>


On Mon, May 2, 2022 at 2:36 PM Chad Young <cyoung at twinstrandbio.com>
wrote:
> Thanks for the quick response. When I try that, I get
>
>  The following packages have unmet dependencies:
>   r-recommended : Depends: r-cran-mass but it is not going to be installed
>                   Depends: r-cran-class but it is not going to be installed
>
> I added explicit installs for both of those (selecting what looked to be
> the most appropriate version) and it seems to be working now.
>
> Chad Young
> Bioinformatics Scientist
> TwinStrand Biosciences <https://twinstrandbio.com/>
>
>
> On Mon, May 2, 2022 at 2:13 PM Dirk Eddelbuettel <edd at debian.org>
wrote:
>
>>
>> On 2 May 2022 at 13:52, Chad Young wrote:
>> | I have a docker file for installing R on Ubuntu 18.04, and as of last
>> week
>> | it is failing. I think it seems to be related to the recent release
of R
>> | 4.2.0. I want to install R 4.1.2, but when I use the below command
and
>> then
>> | check the R version, it comes out as 4.2.0. Do you know why this is
>> | happening?
>> |
>> | RUN apt-get update \
>> |     && apt-get install -y gnupg2 software-properties-common \
>> |     && apt-key adv --keyserver keyserver.ubuntu.com
--recv-keys
>> | E298A3A825C0D65DFD57CBB651716619E084DAB9 \
>> |     && add-apt-repository 'deb
>> https://cloud.r-project.org/bin/linux/ubuntu
>> | bionic-cran40/' \
>> |     && apt-get update \
>> |     && apt-get install -y \
>> |            r-base=4.1.2-* \
>> |            r-recommended=4.1.2-*
>> |
>> | If I just install r-base-core=4.1.2-* it seems to install the correct
>> | version of R.
>>
>> You were close. You need three lines at the end:
>>
>>      && apt-get install -y \
>>             r-base=4.1.2-* \
>>             r-base-core=4.1.2-* \
>>             r-recommended=4.1.2-*
>>
>> This has to do with a fact that such an imposed version does apparently
>> _not_
>> get pushed through to the versions pulled in the by the packages you
>> constrained.  In other words, while 'r-base' gets fixed, the
>> 'r-base-core' is
>> still "free" meaning you get the newest as `apt` tries to be
helpful.
>>
>> Dirk
>>
>> --
>> dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>>
>
	[[alternative HTML version deleted]]

Chad,

I think you have a fundamental disconnect.  "In general" both at CRAN
and in
distros like Ubuntu and Debian you just get rolling releases that will
feature the most current version of packages (with the exception of release
snapshot time at which point a demarcation line is drawn).

So you generally cannot assume you can just randomly impose version constraint.
There are some expections (as the date-snapshots by first MRAN and now RSPM),
but they are generally _not_ integrated with apt.

In short, methinks you cannot assume you can just run a Dockerfile today as
if were a random day you liked between R 4.1.2 and 4.1.3. The repos, and
package management software, are designed for that use case.

Hope this helps,  Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org