A Quick Introduction to liftr

Nan Xiao <https://nanx.me>

2017-12-13

1 Introduction

In essence, liftr aims to solve the problem of persistent reproducible reporting. To achieve this goal, it extends the R Markdown metadata format, and uses Docker to containerize and render R Markdown documents.

2 Metadata for containerization

To containerize your R Markdown document, the first step is adding liftr fields to the YAML metadata section of the document. For example:

---
title: "The Missing Example of liftr"
author: "Author Name"
date: "2017-12-13"
output: rmarkdown::html_document
liftr:
  maintainer: "Maintainer Name"
  email: "name@example.com"
  from: "rocker/r-base:latest"
  pandoc: true
  texlive: false
  sysdeps:
    - gfortran
  cran:
    - glmnet
  bioc:
    - Gviz
  remotes:
    - "road2stat/liftr"
  include: "DockerfileSnippet"
---

All available metadata fields are expained below.

2.1 Required metadata

2.2 Optional metadata

3 Containerize the document

After adding proper liftr metadata to the document YAML data block, we can use lift() to parse the document and generate a Dockerfile.

We will use a minimal example included in the liftr package. First, we create a new directory and copy the R Markdown document into the directory:

path = "~/liftr-minimal/"
dir.create(path)
file.copy(system.file("examples/liftr-minimal.Rmd", package = "liftr"), path)

Then, we use lift() to parse the document and generate the Dockerfile:

library("liftr")

input = paste0(path, "liftr-minimal.Rmd")
lift(input)

After successfully running lift(), the Dockerfile will be in the ~/liftr-minimal/ directory.

4 Render the document

Now we can use render_docker() to render the document into an HTML file, under a Docker container:

render_docker(input)

The function render_docker() will parse the Dockerfile, build a new Docker image, and run a Docker container to render the input document. If successfully rendered, the output liftr-minimal.html will be in the ~/liftr-minimal/ directory. You can also pass additional arguments in rmarkdown::render to this function.

In order to share the dockerized R Markdown document, simply share the .Rmd file. Other users can use the lift() and render_docker() functions to render the document as above.

5 Housekeeping

Normally, the argument prune is set to TRUE in render_docker(). This means any dangling containers or images due to unsuccessful builds will be automatically cleaned.

To clean up the dangling containers, images, and everything without specifying names, please use prune_container_auto(), prune_image_auto(), and prune_all_auto().

If you wish to manually remove the Docker container or image (whose information will be stored in an output YAML file) after sucessful rendering, use prune_container() and prune_image():

purge_image(paste0(path, "liftr-minimal.docker.yml"))

The above input YAML file contains the basic information of the Docker container, image, and commands to render the document. It is generated by setting purge_info = TRUE (default) in render_docker().

6 Install Docker

Docker is an essential system requirement when using liftr to render the R Markdown documents. install_docker() will help you find the proper guide to install and set up Docker in your system. To check if Docker is correctly installed, use check_docker_install(); to check if the Docker daemon is running, use check_docker_running(). In particular, Linux users should configure Docker to run without sudo.