crashes on gamma calculation

[cboettig]

(submitted to me via email)

"I have been trying to duplicate the code from your Methods in EE paper in which you calculate gamma for every tree with branchlengths and that is ultrametric.

When I get to tt <- drop_nontrees(sapply(branchlengths, timetree)), the R session crashes. ("R encountered a fatal error. The session was terminated." is the message in RStudio, but same thing happens in a plain R terminal)

This was happening to me using R 2.15.2, so I just now upgraded to 3.0.0 but the same thing happens.

I'm using a Windows XP x64 machine."

[cboettig]

Crash confirmed address not mapped, appears to be a memory overflow.

• Seems to be a change in ape functions, causing the reorder.phylo in the chronoMPL function to attempt ridiculous memory allocations. Frustrating how fragile much of the ape C code is.
• NOTE The approach shown is not really a robust way to obtain ultrametric trees.
• Potential work-around(?)

library(treebase)
data(treebase)
have <- have_branchlength(treebase)
branchlengths <- treebase[have]
timetree <- function(tree)
  try( chronopl(multi2di(tree), lambda=1))
tt <- drop_nontrees(sapply(branchlengths[1:00], timetree)) # crashes on full set still

gammas <- sapply(tt,  gammaStat)

library(ggplot2)
qplot(gammas)+xlab("gamma statistic")