[BioC] DNAcopy segment() Infinite Loop

[Dario Strbenac]

Hello,

I have some data that I'm segmenting with DNAcopy and the processing enters an infinite loop when it gets to chr13. It's worked for me previously on other datasets, so this could be one of those problems that is hard to track down because it only happens on a certain dataset. But I am hopeful that the maintainer might have the intuition and experience to uncover the cause of it.

Here is a minimal and reproducible example :

library(DNAcopy)
download.file("http://129.94.136.7/file_dump/dario/CNobjects.RData", "./CNobjects.RData") # 3.2 MB
load("CNobjects.RData") # objects 'cn' and 'wts'
segment(cn, weights = wts, verbose = 3)

My session is :

R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DNAcopy_1.26.0

loaded via a namespace (and not attached):
[1] tools_2.13.0


--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia