2019-11-28

Where the packages live

Repository Curation Type VCS Installer
CRAN curated Distr SVN install.packages
Github open Devel git devtools::install_github
Bioconductor curated Both git BiocManager::install
R-forge open? Devel? SVN install.packages with repo set

Comprehensive R Archive Network

Github

  • Get an account (Help)
  • Start a repository
  • Set up an R package (using devtools) and set origin
  • Done

Bioconductor

R for bioinformatics

  • Read the Package guidelines and Coding style

  • Start a repository on Github

  • Write & test your package

  • Submit your package repo to the Bioconductor Contributions repo (Submission process )

  • Maintain:

    • A development branch (master)
    • Current release branch (RELEASE_x_y, currently 3.10)

  • Focused on high-throughput genomic analysis

  • Tightly coupled package versions with bi-annual releases

    • Use their own installer, package BiocManager (on CRAN)
    • Regular, often massive re-installations

  • Run their own git server, but recommend keeping a sync on Github (two remotes)

  • Nice developer ressources

R-forge

  • Run by r-project.org

  • Installation via

install.packages("mypackage", repos = c("http://R-Forge.R-project.org",
"http://your.nearest.CRAN.mirror.org"), dependencies = TRUE)
  • Workflow: ?? Little info visible (without an account?)