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

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