R/qtl: Just Barely Sustainable
R/qtl is an R package for mapping quantitative trait loci (genetic loci that contribute to variation in quantitative traits, such as blood pressure) in experimental crosses (such as in mice). I began its development in 2000; there have been 46 software releases since 2001. The latest version contains 39k lines of R code, 24k lines of C code, and 16k lines of code for the documentation. The continued development and maintenance of the software has been challenging. I'll describe my experiences in developing and maintaining the package and in providing support to users. I'm currently working on a re-implementation of the package to better handle high-dimensional data and more complex experimental crosses. I'll describe my efforts to avoid repeating the mistakes I made the first time around.