Rockerverse

Article about everything related to containers and R, originally based on this blog post, then available as a preprint on arXiv and now published as an article in The R Journal:

Daniel Nüst, Dirk Eddelbuettel, Dom Bennett, Robrecht Cannoodt, Dav Clark, Gergely Daróczi, Mark Edmondson, Colin Fay, Ellis Hughes, Lars Kjeldgaard, Sean Lopp, Ben Marwick, Heather Nolis, Jacqueline Nolis, Hong Ooi, Karthik Ram, Noam Ross, Lori Shepherd, Péter Sólymos, Tyson Lee Swetnam, Nitesh Turaga, Charlotte Van Petegem, Jason Williams, Craig Willis and Nan Xiao. The Rockerverse: Packages and Applications for Containerisation with R. The R Journal (2020), 12:1, pages 437-461. doi:10.32614/RJ-2020-007

The hex sticker uses the font Final Frontier Old Style and the Hubble Ultra-Deep Field combined with the Docker logo as background.

Render the manuscript with Docker

Local build

docker build --tag rockerverse-paper --file .binder/Dockerfile .
docker run -i -v $(pwd):/rockerverse --user $UID rockerverse-paper Rscript -e 'setwd("/rockerverse"); rmarkdown::render("rockerverse.Rmd")'

Image from Docker Hub

docker run -i -v $(pwd):/rockerverse --user $UID nuest/rockerverse-paper Rscript -e 'setwd("/rockerverse"); rmarkdown::render("rockerverse.Rmd")'

Not included projects and packages

• rize, because discontinued, see #35
• docker (https://bhaskarvk.github.io/docker has been removed from CRAN, seems unmaintained by authors
• https://github.com/svlentink/dockerfiles/blob/master/svlentink/r-base-alpine/Dockerfile because the Alpine image is quite a trivial one
• https://github.com/jlisic/R-docker-centos because CentOS images are also provided by R-hub
• sevenbridges includes several Dockerfiles and documentation about using images, and also seems to use Docker in the built workflows but via other tools, not directly, https://sbg.github.io/sevenbridges-r/, https://github.com/sbg/sevenbridges-r/search?p=4&q=docker&unscoped_q=docker
• https://github.com/rocker-jp because it seems to have stalled soon after inception
• https://github.com/thomasp85/fiery because no examples/docs for Docker (though probably trivial anyway)
• RStudio Connect because while it does use a similar mechanism to seperate processes, it does not use Docker and the comparison would require a lot of background explanation, and not all details are available because the software is proprietary
• https://github.com/ecohealthalliance/reservoir is an invididual specific data science image container for a group - add if it fits
• https://itsalocke.com/blog/building-an-r-training-environment/ (one single container for many users in teaching, uses rocker/tidyverse)

Helpers

The README.Rmd file’s source includes some useful little code snippets, e.g. count words or get a list of all contributor’s GitHub handles.