Installing rjags on OSX Mavricks

I am currently working to remove some of the thornier dependencies for BAYSIC (source) and though we have just about managed to replace VCF merge (which has been especially ill behaved for us) we have decided that for now R2jags is still our best bet for Gibbs sampling.

I know some people have a bad time installing RJags but the process below seems to have worked pretty well for me.

First you need to install JAGS, for me this was as easy as downloading and installing:

Once that’s installed we can enter your R console and run:

> install.packages(“rjags”)
> install.packages(“R2jags”)

And there might be one or two dependencies left to install,  I had to run:

> install.packages(‘getopt’)
> install.packages(‘reshape2’)

Finally check if everything is running with:
> library(rjags)

Hope that went well!  Let me know.