Sunday, July 22, 2012

RcppArmadillo and R-forge

Jane Lange and I have recently finished a paper on continuous-time hidden Markov models and published an accompanying R package cthmm on R-forge. Jane's package cthmm relies heavily on Rcpp and RcppArmadillo packages. Somewhat surprisingly, the last dependency caused compilation problems on R-forge. Specifically, the package compiled only on Mac OS X, but not on Linux or Windows. Since Jane and I use Macs, we didn't have any problems compiling the package locally on our computers.

It turns out that the root of the problem was in using Armadillo's .inv() function to invert complex matrices. Armadillo library outsources some of its linear algebra calculations to lapack, which should be no problem since R also relies on lapack (who doesn't, right?). But for some reason systems have only an abbreviated version of the lapack library, missing some functions for complex matrix calculations. This problem is discussed here.

Following suggestions from the above link, my solution was to download missing fortran routines (zgetri.f, ztrti2.f, ztrtri.f) from and add them to /src directory of our package. A bit ugly, but worked and the package compiled on R-forge on all architectures.

P.S. As of July 22, 2012, our cthmm failed to compile on R-forge again, but we believe that this has to do with dependent packages (looks like survival package was not available on Windows). We hope to resolve this problem shortly.

Update on the P.S.: It looks like the problem with the survival package was resolved by the R-forge compilers. Our cthmm compiles now.

Saturday, July 21, 2012

Blog name change

As I find myself working on problems outside of evolutionary biology more often, I decided that a blog name change would be in place. This doesn't mean that I am planning to stop working on phylogenetics and population genetics though.