Liftr Versions Save

Bug Fixes

• Switched to absolute URLs for the contributing guidelines and contributor code of conduct in the readme.

Bug Fixes

• Fixed the issue of parsing Bioconductor package names (#45) for R >= 3.5 and the introduction of BiocManager. We thank Tiago Lubiana for contributing the patch.

Improvements

• Add a new argument dry_run in render_docker() for debugging: when set to TRUE, it will only return the Docker commands and not actually run them.
• New URL for the documentation website: https://nanx.me/liftr/.

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").

Improvements

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

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].

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.

Improvements

• Maintainer email updates.

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.

Bug Fixes

• Correctly rendered the vignette with Pandoc 1.15.0.6.

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.