vobencha / gran

Repository-based tools for reproducibilty at the system-wide installation and individual analysis levels for R

GRANBase

Introduction

GRANBase is an open source set of tools for testing and deploying R packages as package repositories for both general deployment and result reproduction. It is based on the switchr framework, and allows users to deploy package manifests as validated repositories.It is centered around the R repository mechanism for package distribution.

GRANBase provides three major areas of functionality:

• The ability to create one or more R package repositories by pulling and testing packages from diverse locations (SCM, Git, local directory), in a manner conducive to continuous integration
• Tools for recreating specific environments based on sessionInfos, and for creating lightweight virtual repositories which serve the exact package versions specified in the sessoinInfo
• Tools for assessing the potential impact of upgrading a package, to assist administrators in keeping systems up-to-date while protecting reproducibility and comparability of results in long-running core applications

GRANBase performs the following steps when creating or updating a repository. At the end of each step, the packages’ statuses are updated to reflect the results of that step:

• Up-to-date copies of package sources are obtained for each package being built, including updating previously checked-out versions
• Packages whose versions have changed since their last successful build, or who are reverse dependencies of such a package, are built without vignettes into a temporary repository via R CMD build
• Packages which successfully built, along with their GRANBase, CRAN, and Bioconductor-based dependencies are installed into a temporary library location
• Packages which successfully installed are built again, with vignettes, into a staging directory
• Remaining packages are tested via R CMD CHECK, and their statuses are updated accordingly
• Packages which meet the requirements set for the repository (CHECK warnings and notes can be all owed, or not) are deployed into the final destination repository
• The GRANBase manifest is updated to reflect the build results
• An HTML build report is generated from the updated manifest
• The manifest and GRANRepository object are saved
• The GRANRepsitory object is returned

Please refer to the package reference manual and vignettes for more details on usage.

Installation

You may install the stable, release version of GRANBase from CRAN like this:

# Install the CRAN Release Version of GRANBase
install.packages("GRANBase")

Or install the latest development version from GitHub:

# Install using devtools
devtools::install_github("gmbecker/GRANCore",
                         "gmbecker/gRAN")

Contribute

Want to contribute? Great! You can do so by:

• Forking this repo
• Creating a new branch
• Committing changes to that branch
• And finally submitting your changes for review by creating a pull request