use_vignette_docker: Use vignette: Docker

In rworkflows: Test, Document, Containerise, and Deploy R Packages

Use vignette: Docker

Description

Creates a vignette rmarkdown file demonstrates how to create a Docker/Singularity image from a container stored in Dockerhub.

Usage

use_vignette_docker(
  package = names(get_description()),
  docker_org = NULL,
  docker_registry = "ghcr.io",
  cont = construct_cont(cont = paste(docker_org, package, sep = "/"), default_registry =
    docker_registry)[[1]],
  title = "Docker/Singularity Containers",
  vignette_index_entry = "docker",
  save_dir = here::here(),
  path = file.path(save_dir, "vignettes", "docker.Rmd"),
  output = list(`BiocStyle::html_document` = list(md_extensions = "-autolink_bare_uris")),
  port_in = 8787,
  port_out = 8900,
  force_new = FALSE,
  show = FALSE,
  verbose = TRUE
)

Arguments

package	R package name.
docker_org	Docker registry organization name. Can simply be your registry username instead. If NULL, docker_org will be inferred as the R package's GitHub owner.
docker_registry	Docker container registry to push to. Options include: "ghcr.io" : GitHub Container Registry "docker.io" : DockerHub
cont	Which Docker container to use on each OS (NULL means no container will be used for that OS). See here for a list of all official Bioconductor Docker container versions.
title	Title of vignette.
vignette_index_entry	Index entry of the vignette, which is used when creating the navigation bar in the pkgdown site.
save_dir	Directory to save the file to.
path	Path to the file.
output	Vignette output style. Defaults to html_document.
port_in	Port number to route into the docker container. See the Docker docs for further details.
port_out	Port number to route out of docker container. See the Docker docs for further details.
force_new	If the file already exists, overwrite it (default: FALSE).
show	Print the contents of the file in the R console.
verbose	Print messages.

Value

Path to vignette file.

Examples

path <- use_vignette_docker(package = "mypackage",
                            docker_org = "neurogenomics",
                            ## use default save_dir in practice
                            save_dir = tempdir())

rworkflows documentation built on Sept. 23, 2024, 1:08 a.m.