Containerize R Markdown Documents

Persistent reproducible reporting by containerization of R Markdown documents.


Build Status AppVeyor Build Status CRAN Version Downloads from the RStudio CRAN mirror

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.

Installation

Install liftr from CRAN:

install.packages("liftr")

Or try the development version on GitHub:

# install.packages("devtools")
devtools::install_github("road2stat/liftr")

Browse the vignettes or the demo video for a quick-start.

Workflow

Containerize R Markdown Documents with liftr

Events

Time Event Location
July 27, 2017 BioC 2017 (poster for dockflow.org) Dana-Farber Cancer Institute, Boston, MA
May 20, 2017 The 10th China-R Conference (talk) Tsinghua University, Beijng, China
April 18, 2017 DockerCon 2017 (talk) Austin Convention Center, Austin, TX
December 3, 2015 CRI Bioinformatics Workshop (talk) The University of Chicago, Chicago, IL
July 21, 2015 BioC 2015 (workshop) Fred Hutchinson Cancer Research Center, Seattle, WA

Contribute

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

License

liftr is free and open source software, licensed under GPL-3.

News

liftr 0.8 (2017-12-12)

New Features

  • Add a new argument prune in render_docker() to automatically clean up dangling containers and images in case the image build or compilation was not successful (#27). We thank Nicolas Roelandt for suggesting this feature (#25).
  • Added functions prune_container_auto(), prune_image_auto(), and prune_all_auto() for automatic pruning of dangling containers or images without particular names specified.
  • Added function install_docker() for guiding the installation of Docker.
  • Added function check_docker_install()for checking if Docker is properly installed and discoverable.
  • Added function check_docker_running() for checking if Docker daemon is running.

Improvements

  • The argument purge_info was renamed to prune_info in render_docker().
  • Previous functions for cleaning up specific Docker containers and images purge_container() and purge_image() are now renamed to prune_container() and prune_image().
  • RStudio addin: the old addin for removing Docker images was refactored into two new addins: one for removing dangling containers and images, one for removing the successfully built image that corresponds to the current document.
  • Added two new vignettes. Check out vignette("liftr-addins") and vignette("liftr-tidyverse").

liftr 0.7 (2017-09-29)

Improvements

  • Use system font stack instead of Google Fonts in vignettes to avoid pandoc SSL issue.

liftr 0.6 (2017-07-23)

New Features

  • Supports parsing the liftr metadata from a standalone YAML congfiguration file. This feature makes it possible to run liftr without editing the original R Markdown file [#22].

liftr 0.5 (2017-04-11)

New Features

  • Added RStudio addins as shortcuts to containerize and render R Markdown documents.
  • Added new argument cache in render_docker() to improve rendering speed significantly by caching Docker image layers [#18].
  • Added new argument purge_info to render_docker(). This argument controls whether to output the Docker image and container name into an YAML file for purging purposes later.
  • Separate the creation and removal of Docker containers and images: removed the old argument reset in render_docker(); added purge_container() and purge_image() for cleaning up.
  • The ghpkg field is now deprecated. The new remotes field supports devtools remote package name format. Now packages can be installed from GitHub, Bitbucket, Git/SVN servers, URLs, etc.
  • Added new metadata field include for including any custom Dockerfile snippets into the final Dockerfile. This also fixes #21.

Improvements

  • Renamed drender() to render_docker(). drender() is now deprecated.
  • Better naming scheme for liftr metadata fields.
  • Tidy up the output Dockerfile by lift().
  • Added two new examples in inst/examples/: explore tidyverse and Bioconductor RNA-Seq workflow.
  • New website (https://liftr.me) generated by pkgdown, with a full set of function documentation and vignettes available.
  • Added Appveyor support for continuous integration under Windows.
  • Removed Rabix support temporarily to embrace its new version in the future.
  • Added a new demo video.

Bug Fixes

  • Removed -t and -i from docker run to fix #17.

liftr 0.4 (2016-08-05)

Improvements

  • Maintainer email updates.

liftr 0.3 (2015-10-10)

New Features

  • Support specifying CRAN package version precisely.

Improvements

  • Modified examples in documentation to comply with the lastest CRAN Repository Policy.
  • Installing packages with https.

liftr 0.2 (2015-07-30)

Bug Fixes

New Features

  • Added new R Markdown header option pandoc to control Pandoc installation. Automatically set this to false for rocker/rstudio and bioconductor/... images. This solves #12.

liftr 0.1 (2015-07-10)

New Features

  • Initial version of liftr. This version implemented two functions lift() and drender(). They provide basic support for dockerizing R Markdown documents, with support for running Rabix workflows/tools before rendering R Markdown documents in Docker containers.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("liftr")

0.8 by Nan Xiao, 4 months ago


https://liftr.me, https://github.com/road2stat/liftr


Report a bug at https://github.com/road2stat/liftr/issues


Browse source code at https://github.com/cran/liftr


Authors: Nan Xiao [aut, cre] (0000-0002-0250-5673), Miao-Zhu Li [ctb], Teng-Fei Yin [ctb]


Documentation:   PDF Manual  


GPL-3 | file LICENSE license


Imports yaml, knitr, rmarkdown, stringr, rstudioapi

System requirements: Docker (see <https://docs.docker.com/engine/installation/>)


See at CRAN