docs/2019-11-19_installing_packages-notes.md

In 2DegreesInvesting/ds-incubator: Share best practices in coding

title: Installing packages in R author: CJ date: '2019-11-19' slug: installing-packages-notes categories: [] tags: - r description: ''

2019-11-19: Installing packages in R

CJ Yetman

• Installing packages in R is more complicated than it seems

• Structure of a package

  • R files
  • Text based config files
  • Help files
  • Potentially source files in other languages (C, C++, Fortran, etc.)
• Submitted to CRAN, hosted on GitHub, or hosted on other CRAN-like repository (BioConductor, private repos, local etc.)
• Packages are primarily distributed as source packages (raw text files just as you would see in a GitHub repo for a package)
  • BUT… some repos, like CRAN, pre-compile source packages into binaries which are platform specific
• EASY - when you install a binary package (if one is available for your platform), your R environment won’t have to do any processing to make the package work
• EASY - if only a source version of the package is available and the package is written entirely in R (plus various text config files and help files), your R environment should be able to process the package and prepare it for use on your machine without any trouble
• EASY->NIGHTMARE - if only a source version of the package is available and the package includes source files written in a language other than R, your machine will need to be fully setup as a development environment for whatever other languages are used
  • macOS: command line developer tools plus custom clang and fortran
    • https://cran.r-project.org/bin/macosx/tools/
  • Windows: Rtools
    • https://cran.r-project.org/bin/windows/Rtools/

• Suggestion: Install binary packages whenever possible

• remotes::install_github() (devtools::install_github())

  • devtools is a package of tools to help with package development
  • remotes was created from just the install functions of devtools to create a light-weight package for installing from different locations
  • There are numerous remotes::install_* functions
  • These will install packages directly from their development repository
  • Installs as source, with all the potential problems above
  • Sometimes advantageous to get recent bug fixes etc. that have not been released on CRAN yet

2DegreesInvesting/ds-incubator documentation built on Oct. 13, 2021, 10:09 a.m.