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R (rstats) templates for OpenFaaS

This directory contains the stable OpenFaaS R templates.

Template structure

The templates follow a similar structure:

.
├── Dockerfile
├── README.md
├── Rprofile.site
├── function
│   ├── DESCRIPTION
│   └── handler.R
├── index.R
├── install.R
└── template.yml
  • ./Dockerfile: the container is based on this file,
  • ./README.md: description and examples for the template,
  • ./Rprofile.site: R startup options, e.g. repositories, etc.,
  • ./function/DESCRIPTION: R package dependencies for the handler to be edited by the user,
  • ./function/handler.R: R handler to be edited by the user,
  • ./index.R: this is the R entry point receiving the request and outputting the response,
  • ./install.R: utility function used to handle dependencies in the Dockerfile,
  • ./template.yml: stack file specifying the language for the template and the init process for your container, see the YAML reference for additional details.

The files the users are supposed to edit are inside the function folder, users might put other files here that will be copied into the /home/app folder of the Docker image. The handler file usually contains a function called handler that the index.R entry point calls. See the template readme file for specific instructions.

Dependencies

The Dockerfile install script handles dependencies as specified in the DESCRIPTION file in this order:

  1. SystemRequirements: list OS specific sysreqs here, comma separated, these are then installed by the OS's package manager,
  2. CRAN packages listed in Depends:, Imports:, LinkingTo: fields are installed by remotes::install_deps(),
  3. Remotes: fields are installed according to remotes specs, make sure to list the package in Imports: as well, the location specified in Remotes: will be used to get the package from,
  4. VersionedPackages: this field can be used to pin package versions using remotes::install_version(), do not list these packages in other fields (spaces after operators and commas inside parenthesis are important).

An example DESCRIPTION file might look like this:

Package: OpenFaaS
Version: 0.0.1
Imports:
  jsonlite,
  vegan
Remotes:
  vegandevs/vegan
SystemRequirements:
  git-core,
  libssl-dev,
  libcurl4-gnutls-dev
VersionedPackages:
  devtools (>= 1.12.0, < 1.14),
  mypackage (0.1.0)

You can also modify the Dockerfile in the template if specific R version or further customization is needed. The R parent image is defined as a Docker ARG called R_IMAGEthat you can override. I.e. use the versioned Rocker Debian image using custom build arguments: --build-arg R_IMAGE=rocker/r-base:4.0.0, etc. You can also edit the stack YAML file.

The templates are using the following parent images:

  • Debian-based rocker/r-base Docker image from the rocker project for bleeding edge,
  • Ubuntu-based rocker/r-ubuntu Docker image from the rocker project for long term support (uses RSPM binaries),
  • Alpine-based rhub/r-minimal Docker image the r-hub project for smallest image sizes.

System requirements for the same packages might be different across Linux distros. This is a grey area of the R package ecosystem, see rstudio/r-system-requirements, r-hub/sysreqsdb, and https://r-universe.dev/ for help. The maketools R package makes it easy to determine run-time and build-time dependencies for the packages.