Update Docker vs. R blog post

[nuest]

Original post: http://o2r.info/2016/12/15/investigating-docker-and-R/

This issue will be updated with changes so we can have multiple PRs realizing this.

• [x] add shortlink http://bit.ly/docker-r to the top of the post
• [x] add link to containerit presentation and package
• [x] mention nuest/mro images: https://hub.docker.com/r/nuest/mro/
• [x] mention nuest/renjin image: https://hub.docker.com/r/nuest/renjin/
• [x] mention https://www.rdocumentation.org/packages/batchtools/versions/0.9.3
  • uses Docker Swarm as scheduler for HPC systems
  • cluster function starts Docker containers, see https://mllg.github.io/batchtools/reference/makeClusterFunctionsDocker
  • creates docker commands itself, see https://github.com/mllg/batchtools/blob/master/R/clusterFunctionsDocker.R
• [x] add link to PR with these updates to top of the post
• [x] extend information on Rocker and Bioconductor (types of images etc.)
• [x] add sevenbridges package
  • use Docker to create R-based CLIs, see http://www.tengfei.name/sevenbridges/vignettes/docker.html
  • use Docker for testing somehow, see https://www.rdocumentation.org/packages/sevenbridges/versions/1.2.4/topics/set_test_env
• [x] add gitlabr where you can defined the Docker base image for GitLab continuous integration tests, see https://www.rdocumentation.org/packages/gitlabr/versions/0.9/topics/gl_ci_job
• [x] (not sure about this one) rodam-package requires a base software distributed in Docker image or VM, see https://www.rdocumentation.org/packages/Rodam/versions/0.1.2/topics/Rodam-package only mentions you can run the ODAM server based on Docker
• [x] add sanitizers, which uses (Rocker) images to test compiler setups, see https://www.rdocumentation.org/packages/sanitizers/versions/0.1.0
• [x] mention https://bhaskarvk.github.io/docker/ (under dev, very new, wraps Python API so should work on Windows: https://twitter.com/bhaskar_vk/status/884404170631122944, see also https://github.com/wch/harbor/issues/11)
• [x] update link to Boettiger paper to https://dl.acm.org/citation.cfm?doid=2723872.2723882
• [x] mention https://github.com/nuest/x11rockerstudio
• [x] mention plumber: https://www.rplumber.io/docs/docker/

Sources of these: https://www.rdocumentation.org/search?q=docker&packagePage=1&functionPage=4

[bhaskarvk]

FWIW my docker package is now on CRAN and I've unit tested it on Linux & Windows and it should also work under Mac, or for that matter every system where python + docker python module and reticulate R packages are available.

[nuest]

Thanks @bhaskarvk - and congrats for putting the package on CRAN! I'll add a paragraph on your package and will soon try it out!

[nuest]

Some tasks for the next update:

• [ ] review packages from http://rpkg.gepuro.net/ (search for "Docker" and "container")
• [x] mention @akzaidi 's Microsoft R client (see https://github.com/o2r-project/o2r-project.github.io/issues/10#issuecomment-324223027)
• [x] mention Centos & MRO images by https://github.com/jlisic/R-docker-centos
• [x] mention Shinyproxy (https://github.com/openanalytics/shinyproxy and https://www.shinyproxy.io/), which spins up a Docker container with Shiny for every user for isolation and scalability; maybe see also https://github.com/openanalytics/shinyproxy/blob/master/src/main/java/eu/openanalytics/services/DockerService.java
• [ ] update status on fastr, see https://github.com/graalvm/fastr/issues/11#issuecomment-324690911
• [x] add https://github.com/cole-brokamp/rize by @cole-brokamp
• [x] add https://github.com/cboettig/dockermachine by @cboettig

[akzaidi]

Thanks for this super useful post!

I created a docker image for Microsoft R Client here: akzaidi/mrclient-docker. R Client adds to MRO by including a couple of "ScaleR" machine learning algorithms and packages for parallelization and remote computing.

I'm a docker novice, so please let me know if you see any issues or room for improvement!

[nuest]

• [ ] add link to blog post https://rviews.rstudio.com/2018/01/18/package-management-for-reproducible-r-code/ by @colearendt
• [ ] mention https://github.com/ColinFay/dockerfiler by @ColinFay
• [ ] try out https://github.com/richfitz/stevedore by @richfitz and add it to the post
• [ ] add https://github.com/wch/r-debug
• [ ] update information on fastr: image works now, and is on Docker Hub
• [ ] mention Tensorflow image: https://hub.docker.com/r/rocker/tensorflow/
• [ ] Gigantum has own Stack of images and don't use rocker because of licensing, see https://github.com/gigantum/base-images/tree/master/r-tidyverse
• [ ] @noamross is collecting usage of Rocker images in production on Twitter: https://twitter.com/noamross/status/1151254374771019777

[nuest]

The last updates collected here will not be included in the blog post anymore. Instead, take a look at the Rockerverse article: https://github.com/nuest/rockerverse-paper/