1 Deploy R Package on Github

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1.1 Prepare Git and Github

  • Open a free account on Github: comtook comes from “computational toolkits”
  • Install Git: sudo apt-get install git-core
  • Start rstudio
  • Click tools –> global options –> Git/SVN
  • Click Enable version control interface for RStudio projects
  • Sign in Github as the owner/administrator
  • Open a new repository
  • Check the option there to initialize the repository with a README file

1.2 Make R package

  • On Rstudio, File –> New Project –> Create a new project from Version Control
  • Choose Git
  • Provide the repository URL including the new repository name: https://github.com/comtook/afmFreeEnergy
  • Choose a project directory name on my local computer: afmFreeEnergy
  • Click Create Project
  • Change to use devtools tools: library(devtools)
  • Create the package skeleton with devtools::create(‘~/afmFreeEnergy’)
  • Choose Overwrite files
  • Edit the information in DESCRIPTION
  • Put my codes in the R/ subdirectory
  • Copy raw data in the folder inst/extdata
  • Re-load packge with devtools::load_all()
  • Re-generate documentation and namespace: devtools::document(‘/path/to/pkg’)
  • Build binary: devtools::build()
  • Install: devtools::install(‘/path/to/pkg’)
  • Re-load: library(‘pkg’)

1.3 Publish my R package on Github

1.4 Install R package from Github

  • library(devtools)
  • install_github(“comtook/afmFreeEnergy”) or
  • sudo su - -c “R -e "devtools::install_github(‘comtook/afmFreeEnergy’)\”"

1.5 Specify version

  • to use the “double colon” approach
  • Imports: data.table (>= 1.9.4), dplyr

1.6 Delete repository on Github

  • Sign in as the owner/administrator
  • On GitHub, navigate to the main page of the repository
  • Under your repository name, click Settings
  • Scroll down to “Danger Zone” and click “Delete this Repository”
  • Follow the instruction
  • On your local machine, delete .git directory/folder within the repository’s directory