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r-dependent-packages

README.md

R packages from the DESCRIPTION file (via pak) (r-dependent-packages)

This Feature sets scripts to install dependent R packages from the DESCRIPTION file in the repository.

Example Usage

"features": {
    "ghcr.io/rocker-org/devcontainer-features/r-dependent-packages:0": {}
}

Options

Options Id Description Type Default Value
when When to install the dependent R packages? Each option corresponds to the lifecycle scripts. 'skip' means to skip the installation. string postCreate
pakVersion Version of pak to install. By default, the stable version is installed if needed. string auto
manifestRoot The root path of the DESCRIPTION file recording the dependent R packages. Passed to the root argument of the pak::local_install_deps() function. string .
additionalRepositories String passed to the pak::repo_add() function. string -
dependencyTypes Comma separated list of dependency types to install. Passed to the dependencies argument of the pak::local_install_deps() function. string all

System Requirements

Please use this with an R-installed image (e.g. ghcr.io/rocker-org/devcontainer/r-ver) or this should be installed after installing Features that installs R (e.g. ghcr.io/rocker-org/devcontainer-features/r-apt, ghcr.io/rocker-org/devcontainer-features/r-rig).

"features": {
    "ghcr.io/rocker-org/devcontainer-features/r-rig:1": {},
    "ghcr.io/rocker-org/devcontainer-features/r-dependent-packages:latest": {}
}

DESCRIPTION file format

This feature installs packages listed in the manifest file named DESCRIPTION. If you are new to the DESCRIPTION file, please refer to the usethis::use_description() function's reference.

Here is an minimal example of the DESCRIPTION file. At least, the Package and Version fields are required. The Imports field is a list of packages that will be installed.

Package: foo
Version: 0.0.0.9000
Imports:
    cli,
    rlang

Additional fields

When developing an R package, we may want to specify dependencies that are only needed during development in the DESCRIPTION file. In such cases, we can use any field name starting with Config, and generally specify multiple fields prefixed with Config/Needs as follows:

Package: foo
Version: 0.0.0.9000
Suggests:
    cli
Config/Needs/website:
    curl
Config/Needs/dev:
    crayon

If we want use such fields to install dependencies, we can specify the dependencyTypes field of this Feature like this:

"ghcr.io/rocker-org/devcontainer-features/r-dependent-packages:latest": {
    "dependencyTypes": "all,Config/Needs/website,Config/Needs/dev"
}

Environment variables

Enviroment variables listed in the containerEnv field are used in the package installation process. See the reference of the pak package for options for pak.

"containerEnv": {
    "NOT_CRAN": "true",
    "PKG_CRAN_MIRROR": "https://cloud.r-project.org/"
}

Cache directory and cache volume

The package cache directory in the container is set to /pak/cache.

This directory is stored in a volume named devcontainer-pak-cache and is shared among multiple containers.

See also

References

Note: This file was auto-generated from the devcontainer-feature.json. Add additional notes to a NOTES.md.