R Requirements

Specify which R packages should be available in order to run the component.

Example:

setup: 
  - type: r
    cran: anndata
    bioc: [ AnnotationDbi, SingleCellExperiment ]
    github: rcannood/SCORPIUS

bioc

Type: String / List of String

Default: Empty

Specifies which packages to install from BioConductor.

Example:

bioc: [ AnnotationDbi ]

bioc_force_install

Type: Boolean

Default: False

Forces packages specified in bioc to be reinstalled, even if they are already present in the container. Default: false.

Example:

bioc_force_install: false

bitbucket

Type: String / List of String

Default: Empty

Specifies which packages to install from Bitbucket.

Example:

bitbucket: [ org/package ]

cran

Type: String / List of String

Default: Empty

Specifies which packages to install from CRAN.

Example:

cran: [ anndata, ggplot2 ]

git

Type: String / List of String

Default: Empty

Specifies which packages to install using a Git URI.

Example:

git: [ https://some.git.repository/org/repo ]

github

Type: String / List of String

Default: Empty

Specifies which packages to install from GitHub.

Example:

github: [ rcannood/SCORPIUS ]

gitlab

Type: String / List of String

Default: Empty

Specifies which packages to install from GitLab.

Example:

gitlab: [ org/package ]

packages

Type: String / List of String

Default: Empty

Specifies which packages to install from CRAN.

Example:

packages: [ anndata, ggplot2 ]

script

Type: String / List of String

Default: Empty

Specifies a code block to run as part of the build.

Example:

script: |
  cat("Running custom code
")
  install.packages("anndata")

svn

Type: String / List of String

Default: Empty

Specifies which packages to install using an SVN URI.

Example:

svn: [ https://path.to.svn/group/repo ]

type

Type: String

Specifies the type of the requirement specification.

url

Type: String / List of String

Default: Empty

Specifies which packages to install using a generic URI.

Example:

url: [ https://github.com/hadley/stringr/archive/HEAD.zip ]

warnings_as_errors

Type: Boolean

Default: True

Specifies whether to treat warnings as errors. Default: true.

Example:

warnings_as_errors: true