R

I recently updated my set-up, and because I use a High-Performance cluster from my University (kudos to avakas) to run various simulations and analyses, I have MPI and Rmpi installed on my laptop in order to test my scripts before submitting them to the big cluster. So I installed openmpi from homebrew very easily: brew update brew install open-mpi But then I had extensive trouble installing the Rmpi package…

I just released a new package on CRAN. It’s called NPflow, it performs Dirichlet process mixture of multivariate normal, skew-normal or skew t-distributions modeling, you should check it out. I was a little worried because the check from Travis CI was returning a NOTE. And even though the NOTEs seem like mild problems, “you should strive to eliminate all NOTEs” before submitting to CRAN ! Preparing for an email exchange with a member of the R core team, I wrote the following in the submission comments:

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 ships with a clang compiler that does not support openMP. So first one needs to install gcc (from homebrew for instance).

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 !

At Bordeaux University, we are quite lucky. I mean as computational consumers. Indeed, we have access to a big CPU cluster, a mesocenter that has been build for all the researchers in the Aquitaine area (in the south west of France). And it’s a big one. It’s named avakas, and it has brought my Ph.D. computational projects to an other scale ! But for a few month now, I have also been granted access (for free as a I work in a national research agency) to a new kind of big computer: a net of heaters.

Last week, a colleague draw my attention on this new log files from the Rstudio cloud CRAN mirror, through a post from Tal Galili. This CRAN mirror is a little different, as it uses Amazon CloudFront to deliver the downloads rapidly from a server near you, wherever that is. But what’s really great about it, is the availability of those log files, that have been recording every package download since October 2012, daily!