[BioC] Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file

[Stephen Turner]

Lukas, and others:

I'm trying to use the MEDIPS package to look for differentially
methylated regions, supplying a regions of interest file (essentially
a bed file). I was able to successfully run MEDIPS.methylProfiling
supplying the frame_size=500 argument to look for DMRs in 500-bp
windows. Now I'd like to supply my own regions of interest to look for
DMR around genes that are differentially expressed from microarray.

I get the following segfault:

###############
> dmrGenes <- MEDIPS.methylProfiling(data1=CONTROL.SET, data2=BPA.SET, ROI_file="ROI_file.txt", select=2)
Preprocessing...
Reading ROIs...
Extract data according to given ROI...
Differential methylation will be calculated on the ROI data set
Analysed 379 / 2893
 *** caught segfault ***
address 0x2b61ee9d5e98, cause 'memory not mapped'

Traceback:
 1: .Call("roiprofile", input, as.numeric(select), as.matrix(ROI2),
 as.integer(chr_binposition), data1, data2, environment(wilcox.test),
   wilcox.test, environment(var), var, environment(math), math,
t.test, environment(t.test), as.numeric(factor(chr_names(data1))))
 2: withCallingHandlers(expr, warning = function(w)
invokeRestart("muffleWarning"))
 3: suppressWarnings(.Call("roiprofile", input, as.numeric(select),
 as.matrix(ROI2), as.integer(chr_binposition), data1, data2,
environment(wilcox.test), wilcox.test, environment(var),     var,
environment(math), math, t.test, environment(t.test),
as.numeric(factor(chr_names(data1)))))
 4: MEDIPS.methylProfiling(data1 = CONTROL.SET, data2 = BPA.SET,
ROI_file = "ROI_file.txt", select = 2)
aborting ...
###############

I ran this on a machine with 128GB RAM, so I know that wasn't the
problem. It looks like the segfault was happening with line 379 in the
sample above. I went into the regions of interest (ROI) file
containing gene coordinates. Nothing looked weird about this line, but
I deleted it anyway. When re-running, I still get segfaults, just at
different positions.

Thanks for any insight you might have.
Stephen


> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
[1] BSgenome.Mmusculus.UCSC.mm9_1.3.19 MEDIPS_1.8.0
[3] BSgenome_1.26.1                    Biostrings_2.26.3
[5] GenomicRanges_1.10.6               IRanges_1.16.4
[7] BiocGenerics_0.4.0

loaded via a namespace (and not attached):
[1] gtools_2.7.0    parallel_2.15.2 stats4_2.15.2