OpenMP, OS-X and R

This is a quick technical post, that is as much about disseminating the information as putting it in a place where I can find it again in the future. I have been trying to use openMP in an R package that I am currently developing. OpenMP is supported by the popular gcc compiler. However, OS-X Xcode now ship with a clang compiler that does not support openMP. So first one needs to install gcc (from homebrew for instance). The thing is then to get R to actually use this gcc compiler. After many hours of struggle, I got it working by modifying the “~/.R/Makevars” file, in which clang must be replaced by gcc (or gcc-$version).

In the case where there is no .R folder and/or Makevar file, just create one. In order to replace clang by gcc, the two following lines suffice:


gcc-4.9 can of course be replace by any other compiler  you might want to use ( such as another version of gcc for instance), and an absolute path to the compiler can also be specified (see comment from kamvarz below)

RcppAramdillo & OS X Mavericks configuration

I am in the process of speeding up some code, and I have been lured by the promises of Rcpp. Since the functions I am working on are mainly linear algebra, I wanted to try out RcppArmadillo. This put my googling skills to a test as I spent (way) too much time trying to figure out errors until I found this post. Thank you James Balamuta ! Be warned RcppArmadillo, microbenchmarking is on !

What is Statistics ?

The American Statistical Association launched a new website thisisstatistics with general information on what being a statistician really means today. I often meet fearful looks when I meet people and present myself as a “biostatistician” (the key word being statistician here). Up to the point that I now generally say I work in “applied mathematics in medicine”, before I drop the magical “big data” keyword in the necessary explanation following this title.

This website seems very easy to navigate, and I hope it will participate in the heat statistics are getting, being the sexiest job this days !

Check out the 2 short videos below: