Do not use this repo or formula. Instead, you should use this repo

Customizable R formula for Homebrew

This is a custom Homebrew R formula that enables OpenBLAS and OpenMP for accelerated linear algebra. It does not require X11/XQuartz and instead relies on Cairo for graphics support. It includes dependencies listed in this blog post by Benjamin T. Skinner.

On macOS, you must first install XCode Command Line Tools, but this should be installed with Homebrew. Seth Fore's version also includes Tcl-Tk by default, but we do not require it. There is also optional support for IUC, Java, Pango, and TexInfo, but none of these are strictly required.

Installation

This modified R formula can be installed as follows.

Add the repository to your homebrew

brew tap cole-trapnell-lab/r-srf

Check available installation options

brew info cole-trapnell-lab/r-srf/r

Compile the modified R formula:

brew install cole-trapnell-lab/r-srf/r

You should also install the cmake cask so you can install some R packages:

brew install --cask cmake

Check if the default R is correct by running which R. It should be $(brew --prefix)/bin/R, e.g. /opt/homebrew/bin/R. You might have to start a new terminal session for it to take effect.

Once installed, the compiled dependencies can be checked by invoking R and running capabilities(). You can test if everything is as expected with the following:

all(capabilities == c(jpeg = TRUE,
					  png = TRUE,
					  tiff = TRUE,
					  tcltk = FALSE,
					  X11 = FALSE,
					  aqua = TRUE,
					  `http/ftp` = TRUE,
					  sockets = TRUE,
					  libxml = FALSE,
					  fifo = TRUE,
					  cledit = TRUE,
					  iconv = TRUE,
					  NLS = TRUE,
					  Rprof = TRUE,
					  profmem = TRUE,
					  cairo = TRUE,
					  ICU = TRUE,
					  long.double = FALSE,
					  libcurl = TRUE)
)

If the result of the above is not TRUE, check the individual capabilities():

       jpeg         png        tiff       tcltk         X11        aqua
       TRUE        TRUE        TRUE       FALSE       FALSE        TRUE
   http/ftp     sockets      libxml        fifo      cledit       iconv
       TRUE        TRUE       FALSE        TRUE        TRUE        TRUE
        NLS       Rprof     profmem       cairo         ICU long.double
       TRUE        TRUE        TRUE        TRUE        TRUE       FALSE
    libcurl
       TRUE

Once the capabilities are properly set, you can safely uninstall previous versions of R. You may have to reinstall your R libraries.

R/X11 support deprectation notice

While I won't be immediately deprecating X11 supported R builds, I am currently unlikely to continue maintaining them at some point in the future. For those affected by this, please refer and post any comments to this discussion thread. All notices pertaining changes to R/X11 support will be posted here or in the relevant discussion. If you have any thoughts, suggestions or concerns surrounding how/when this process will take place, I highly recommend contributing to the discussion.

Note for R Developers

I am open to suggestions on how to improve the functionality of this formula. I am not a programming expert and welcome any tested solutions that enhance the functionality of this formula, specifically with reference to issues related to changes in recent Xcode and CLT deployments.