R SIG Debian - Jul 2024 - Issues with Ubuntu 22.04 and Installing the Latest Version of R (R 4.4.1) to Docker Image

Hi Dirk and Marco,

I need to test some of the suggested solutions and circle back here.

Thank you so much for your help.

Br,
Lauren
--
Lauren J. Gerber
Bioinformatician
Precision Systems Medicine (Kallioniemi) Research Group
iCAN ? Digital Precision Cancer Medicine Flagship
Institute for Molecular Medicine Finland (FIMM)
Nordic EMBL Partnership for Molecular Medicine
Biomedicum Helsinki 2U, D301a1
P.O. Box 20 (Tukholmankatu 8)
FI-00014 University of Helsinki, Finland
lauren.gerber at helsinki.fi

From: Dirk Eddelbuettel <edd at debian.org>
Date: Tuesday, 9. July 2024 at 9.13
To: marcoblanchette at icloud.com <marcoblanchette at icloud.com>
Cc: Dirk Eddelbuettel <edd at debian.org>, Gerber, Lauren J
<lauren.gerber at helsinki.fi>, r-sig-debian at r-project.org
<r-sig-debian at r-project.org>
Subject: Re: [R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest
Version of R (R 4.4.1) to Docker Image

On 8 July 2024 at 21:01, marcoblanchette at icloud.com wrote:
| No sure why you?re doubting me but if one would like the minimal Dockerfile
| following the CRAN recommendations at https://cloud.r-project.org/bin/linux/
| ubuntu/, one would simply do

I am aware. I co-wrote those instructions. The Dockerfile I pointed to is
newer, and regularly used by me and others.

I still think you continue to answer questions that Lauren did not ask:
nobody has stepped in to replicate _her issue_ starting from a different
container. But inasmuch as you also try to help it is of course appreciated.

But maybe it is time to wait for Lauren to chime about what works, and what
doesn't.

Dirk

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

	[[alternative HTML version deleted]]

Lauren,

I am now back home where looking into these things is a little easier. From
your first email to me, I started off with the selenium container you
mentioned as your starting point.

And that basically is your issue. It is a 'high-level' container, and it
sets
a user. (Essentially) all other Dockerfiles you have seen and been pointed at
are 'lower-level' and operate as root -- so you need to inject
'sudo' calls.
Otherwise it really is 'just' getting one key and adding one repo, but
it
helps to have had the same user <-> root issues before ...

So below is a working 'minimal' Dockerfile that gets me R 4.4.1
(validated
via 'docker exec -ti container_id_here bash' once built). Hope it helps.

Best,  Dirk



FROM selenium/standalone-firefox:latest

## Following the standard rocker/r2u:jammy Dockerfile, and adapted slightly

RUN sudo apt update \
##
## We would normally do
##   apt install --yes --no-install-recommends ca-certificates locales wget
## but these are already installed
##
## So we skip to the next step of adding the key and repo
   && wget -q -O -
https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
           | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc  \
   && echo "deb [arch=amd64
signed-by=/etc/apt/trusted.gpg.d/cran_ubuntu_key.asc]
https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" \
           | sudo tee -a /etc/apt/sources.list.d/cran.list \
##
## Update again and install R
   && sudo apt update -qqq \
   && sudo apt install --yes --no-install-recommends r-base-core


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