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

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
>
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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
>>
>
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