Installing mcmcse on a Mac

For reasons not worth going into, I wanted to install the R package mcmcse. This became a pain thanks to its dependency fftwtools, so I didn’t do it for weeks. For posterity, and in case it helps anyone else, here’s what I had to do to install fftwtools on a Mac (an M1 Mac in particular).

(I seem to recall difficulties of a similar nature when I wanted to get mcmcse working on Ubuntu as well.)

TL;DR

This is really just a note on ways to point R to things it doesn’t know where to look for or can’t find. The short version is: you can run system("PATH=/path/to/whatever:${PATH}") to add something to the PATH from inside an R session just long enough for R to find it and install it. If R needs that every time, I do not have the solution here, but it probably involves the .Renviron file.

Tip: disable auto updating

This saga will require, potentially, running brew install. For reasons I cannot fathom, this auto updates things. Because I’m lazy, I installed R with homebrew, which means when it auto-updates packages, my entire goddamn R installation gets shot to hell. The umpteenth time this happened and I got the equivalent of “new R who dis?” when I went to load packages I used daily, I figured out how to make it stop. Now I only call homebrew with the HOMEBREW_NO_AUTO_UPDATE=1 flag enabled, as HOMEBREW_NO_AUTO_UPDATE=1 brew install <whatever>. More on this here.

Overcoming pkg-config errors

The first error I encountered was that pkg-config could not be found. Assuming that you have it installed already (I did, otherwise you want HOMEBREW_NO_AUTO_UPDATE=1 brew install pkg-config), the solution can be found here which links to information here which outsources some explanation here.

The short version: somewhere you need to get the place pkg-config is added to your PATH.

I tried creating .Renviron to set this for R in perpetuity, but it didn’t seem to work. I probably should have figured out why, but instead I opted for a bandaid to just get the damn thing to install, and ran system("PATH=/opt/homebrew/bin:${PATH}") in R.

That worked, and revealed another problem.

You need fftw

The package fftwtools is an interface to the library fftw, so you need to have that. If you don’t, run HOMEBREW_NO_AUTO_UPDATE=1 brew install fftw.

Victory is life

Congratulations, you can now install mcmcse. Have fun!