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 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 --entrypoint /bin/bash <image>

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

To install quarto, either download the .deb listed here via an entrypoint, and install it:

ADD https://github.com/quarto-dev/quarto-cli/releases/download/v1.6.40/quarto-1.6.40-linux-amd64.deb /tmp/quarto.deb
RUN dpkg -i /tmp/quarto.deb && rm /tmp/quarto.deb

Or follow the posit instructions to get the latest version.

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

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

List of INBO Packages

• checklist

• inbodb

• inborutils

• inbospatial

• n2khab

• watina << inbodb

• INBOmd << checklist

• INBOtheme

• INLA <- fmesher

• n2kanalysis << n2khelper multimput < INLA < fmesher

• all in one

  • tidyverse
  • bookdown?

(publish to docker hub?)

Testing

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

docker run -it --entrypoint /bin/bash <image>
R --vanilla --silent -q -e 'library("<image>")'

Remove all images:

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

Notes

• 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

n2kanalysis <- ‘multimput’, ‘n2khelper’, ‘RODBC’ libcurl4-openssl-dev libgit2 libssl-dev libudunits2-dev cmake libxml2-dev sql.h and sqlext.h via unixodbc-dev? INLA