I’ve long needed to revise the function
scantwo, for performing a two-dimensional genome scan for pairs of loci. I was looking at the function today, and was aghast to find that it's 1354 lines long. That's 4% of the R code in the package!
And the R code is just moving data and results around; the actual calculations are in C (in a series of files that comprise 4725 lines — 20% of the C code in the package).