Chapter 9 Set up an R dev environment

There are two different types of R packages you can install, binary packages and source packages. When you install released packages from CRAN using install.packages() you are installing binary packages.1 When you install development packages using devtools::install_github() you are installing source packages.

We recommend the devtools package to install source packages from GitHub and elsewhere, and also to install (and develop) packages you may write yourself.

devtools can be installed from CRAN like any other package.

Once a binary or source package is installed they are identical, however source packages which include C/C++ or Fortran code require additional tools to install, so there is additional system preparation needed.

9.1 Windows: system prep

On Windows the compiler collection needed for installing packages from source is called Rtools.

Rtools is NOT an R package, so it is not installed with install.packages(). Instead download it from http://cran.r-project.org/bin/windows/Rtools/ and run the installer.

During the Rtools installation you will see a window asking you to “Select Additional Tasks”.

  • Do not select the box for “Add rtools to system PATH”, devtools and RStudio should put Rtools on the PATH automatically when it is needed.
  • Do select the box for “Save version information to registry” (it should be selected by default).

9.2 macOS: system prep

On macOS you will need to install the Xcode Command Line Tools, which may already be installed. You can check if they are by running

If they are not installed you have a few options.

  • Minimalist approach (what I do): Install Xcode Command Line Tools. In the shell:

    xcode-select --install

  • Install the current release of full Xcode from the Mac App Store. WAY more stuff than you need but the advantage is App Store convenience.

9.3 Verify system prep

If this function runs without error then congratulations, your R installation is properly set up!

9.4 What about Homebrew?

Users on macOS often install R with homebrew via this formula:

Unfortunately, when R is installed in this way it is not compatible with the CRAN package binaries, which means you must build and install all packages from source. This takes additional time during installation and can lead to more time spent dealing with installation issues if a package fails to compile.

Instead, if you prefer the convenience of homebrew, we recommend installing the r cask. NOTE: the cask used to be named r-app but the -app suffix was dropped due to a homebrew policy change around 2019-03-11.

This will install the CRAN R distribution, so all package binaries will be available just like they would be from installing R manually.

9.5 What about Conda?

Some users use conda in python contexts and notice that conda now also provides (some) R package binaries.

However we would suggest avoiding conda at this time, only a limited number of all CRAN packages are available2 and many users run into installation problems trying to use install.packages() inside conda environments. Using install.packages() also means you no longer declare all dependencies in the same location. Which means your work is less reproducible than if you always install only conda packages.

For these reasons we suggest you either restrict yourself only to packages available as official conda packages, or avoid using conda for R.

  1. On Linux there are no binary packages, so install.packages() will instead install source packages.↩

  2. ~1,500 out of ~13,000 as of this writing↩