contaINBO

This repository is a collection of Dockerfiles to support you to bring your favorite INBO packages to containers, such as Docker or Podman.

The dockerfiles are organized in subfolders; each contains the minimum prerequisites for creating a container based on Rocker images. The underlying OS is Ubuntu which in turn builds on Debian Testing. Scripts are tested with r-base, but should be portable to rocker/rstudio.

docker pull docker.io/r-base

A tutorial on containerization is in the making: https://github.com/inbo/tutorials/tree/dev_docker.

You can consolidate these dockerfiles on demand to derive your own container builds. The list is incomplete, but you might find similar packages. I am accumulating additional examples as I move on. Feel free to contribute.

Tips and Tricks

all updates

You might want to update system packages upon building:

# update the system packages
RUN apt update \
    && apt upgrade --yes
    
# update pre-installed R packages
# RUN Rscript -e 'update.packages(ask=FALSE)'

terminal access

You can access the container terminal as follows:

docker run -it <image> bash

pak and r2u

Using R package managers might simplify Dockerfiles and save you time.

Here is how you can introduce pak to your build:

• https://pak.r-lib.org

RUN R -q -e 'install.packages("pak", dependencies = TRUE)'
RUN R -q -e 'pak::pkg_install("<package>")' 

For r2u, there is a rocker image which you can use as a base for your custom containers.

• https://github.com/rocker-org/r2u

docker run -it docker.io/rocker/r2u

private repos

If you require private repo's within the container, copy them in as follows:

# copy the repo
COPY my_private_repo /opt/my_private_repo

# manually install dependencies
RUN R -q -e 'install.packages("remotes", dependencies = TRUE)' # just an example

# finally, install package from folder
RUN R -q -e 'install.packages("/opt/my_private_repo", repos = NULL, type = "source", dependencies = TRUE)'

quarto

Quarto is available on some pre-packed rocker images (e.g. rocker/rstudio). However, you might prefer the latest version, or adjust system integration. Option 1: To install quarto from a debian package, either download the .deb listed here via an entrypoint, and install it:

ADD https://github.com/quarto-dev/quarto-cli/releases/download/v1.7.13/quarto-1.7.13-linux-amd64.deb /tmp/quarto.deb
RUN dpkg -i /tmp/quarto.deb && rm /tmp/quarto.deb

Check quarto releases regularly to get the latest version: https://github.com/quarto-dev/quarto-cli/releases

Option 2: follow the posit instructions to get the latest version of quarto.

Option 3: Or use git and follow instructions here. (Requires xz-utils.)

git clone https://github.com/quarto-dev/quarto-cli
cd quarto-cli
./configure.sh

Additional modules will certainly be useful:

RUN quarto install tinytex --update-path
RUN python3 -m pip install jupyter

You can log into the bash and run quarto check for a checkup and further extensions.

renv

• rstudio/renv#446

When attampting docker-compose, see note here: rstudio/renv#599

geocomputation

https://github.com/geocompx/docker https://github.com/geocompx/docker/blob/master/dockerfiles/Dockerfile_ubuntugis_unstable

RUN apt-get update \
	&& apt-get install -y --no-install-recommends \
		software-properties-common \
		vim \
		wget \
		ca-certificates \
  && add-apt-repository --enable-source --yes "ppa:marutter/rrutter3.5" \
	&& add-apt-repository --enable-source --yes "ppa:marutter/c2d4u3.5" \ 
	&& add-apt-repository --enable-source --yes "ppa:ubuntugis/ubuntugis-unstable" 
RUN apt-get update \
  && apt-get install -y --no-install-recommends \
 	  libudunits2-dev libgdal-dev libgeos-dev libproj-dev # liblwgeom-dev
# install the r-spatial stack linking to new OSGeo pkgs
RUN R -e 'install.packages(c("sf", "lwgeom", "rgdal", "sp", "stars"))'

List of INBO Packages

• checklist

• inbodb

• inborutils

• inbospatial

• multimput

• n2khab

• watina << inbodb

• INBOmd << checklist

• INBOtheme

• INLA <- fmesher

• inlatools

• n2kanalysis << n2khelper multimput < INLA < fmesher

• all in one

(publish to docker hub?)

Testing

• create a dockerfile
• build it
• enter the terminal and run R

docker run --name <container-name> -it <image> bash
# e.g. # docker run --name bash-quicktest -it docker.io/rocker/r-base bash
R --vanilla --silent -q -e 'library("<package>")'

Remove all images:

docker rmi $(docker images -q)
# or
podman rmi $(podman images -q) -f

Notes

Github has rate limits. If you encounter a 403 upon github installation, wait and repeat.

• httr <- libcurl4-openssl-dev libssl-dev
• xml2 <- libxml2
• units <- libudunits2-dev
• rgbif <- libssl-dev libudunits2-dev libxml2 ++libprotobuf-dev
• sf <- a whole lot of stuff, incl. units
• usethis <- openssl, curl, credentials, httr2, gert, gh
• pkgdown <- libharfbuzz-dev libfribidi-dev, lib8-dev
• devtools <- ‘usethis’, ‘pkgdown’, ‘rcmdcheck’, ‘roxygen2’, ‘rversions’, ‘urlchecker’
• magick <- libmagick++-dev
• gt <- juicyjuice <- lib8-dev
• ragg <- libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
• checklist <- [usethis, pkgdown, devtools] + librdf0-dev libsodium-dev
• INBOtheme <- libssl-dev libcurl4-openssl-dev git libgit2-dev
• INBOmd <- [checklist, INBOtheme] + libpoppler-cpp-dev
• INLA <- [fmesher devtools] + jags
• n2kanalysis <- [multimput n2khelper RODBC INLA] libcurl4-openssl-dev libgit2 libssl-dev libudunits2-dev cmake libxml2-dev unixodbc-dev
• multimput <- INLA

INLA temporary issue?

# RUN R -q -e 'install.packages("HKprocess", repos = c("https://inlabru-org.r-universe.dev", "https://cloud.r-project.org"))'
# 'HKprocess’ https://cran.r-project.org/web/packages/HKprocess/index.html archived!