diversitree OS X Mavericks install

instructions.md

Installing diversitree on OS X Mavericks, R 3.1.0

I installed R from the installer on CRAN

If you installed R from the installer on CRAN:

The easy way

Download my compiled package from Dropbox and install it that way:

curl -O https://dl.dropboxusercontent.com/u/8859543/diversitree_0.9-7.tgz
R CMD INSTALL diversitree_0.9-7.tgz

This bundles everything that you need for diversitree, including GSL and FFTW for QuaSSE support.

The hard way

First install GSL, Fortran, and FFTW (optional) using Homebrew:

brew install gsl gcc fftw

GSL and GCC are bottled so it should be as fast as your download speed. Compiling FFTW will take a while so you don't need to do it unless you need it for QuaSSE.

R thinks everyone has the same setup everywhere. So it'll look for gfortran-4.8 even though a perfectly servicable gfortran is available. As far as I can tell there is no way to change this in R CMD INSTALL using command line arguments. So instead we will hack into R's configuration files.

First confirm that gfortran is installed and working:

gfortran --version

Then find out where GCC's libraries live:

gfortran -print-libgcc-file-name

I get /usr/local/Cellar/gcc/4.8.3/lib/gcc/x86_64-apple-darwin13.2.0/4.8.3/libgcc.a; this might be different on your machine. You'll need this for later.

Now, edit R's configuration variables:

vim /Library/Frameworks/R.framework/Resources/etc/Makeconf   ## or nano, mate, etc.

Edit the lines starting with FC, F77, and FLIBS. Mine currently look like:

FC = gfortran-4.8
F77 = gfortran-4.8
FLIBS =  -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm

Replace FC and F77 with just gfortran. Replace the long path after -L in FLIBS with the output of gfortran from above, without the libgcc.a bit at the end. Mine now look like:

FC = gfortran
F77 = gfortran
FLIBS =  -L/usr/local/Cellar/gcc/4.8.3/lib/gcc/x86_64-apple-darwin13.2.0/4.8.3/ -lgfortran -lquadmath -lm

Now download and install the source tarball for diversitree:

curl -O http://cran.rstudio.com/src/contrib/diversitree_0.9-7.tar.gz
R CMD INSTALL diversitree_0.9-7.tar.gz

I installed R from source

I hope you used Homebrew. Assuming the install of R went well (that is, brew install r didn't vomit everywhere) and you didn't nuke your build setup in the meantime, you should just need to install gsl (brew install gsl) and optionally fftw (brew install fftw) and install.packages("diversitree") should 'just work'.