[R-sig-Debian] Installing R 4.1.2 doesn't work as it did a week ago
Chad Young
cyoung @end|ng |rom tw|n@tr@ndb|o@com
Mon May 9 16:41:48 CEST 2022
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 using 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 using 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 using debian.org
>>
>
[[alternative HTML version deleted]]
More information about the R-SIG-Debian
mailing list