Hi all,

I'm trying to run countOverlaps on two GRanges objects and I am getting a segfault.  The error isn't too consistent (occasionally it works properly), but the following bit of code seems to reproduce the error every time I run it. I'm not sure what could be causing this behavior, but any help would be greatly appreciated.

Thank you,

Stephen

> library(GenomicRanges)
> con <- url("https://dl.dropboxusercontent.com/u/34782695/djfrag.rda")
> load(con)
> dj <- djfrag$dj
> fragments <- djfrag$fragments
> set.seed(1234)
> replicate(2, countOverlaps(dj, fragments))

 *** caught segfault ***
address 0xa2a7f58, cause 'memory not mapped'

Traceback:
 1: .Call(.NAME, ..., PACKAGE = PACKAGE)
 2: .Call2("NCList_find_overlaps_in_groups", start(q), end(q), q_space,     q_groups, start(s), end(s), s_space, s_groups, nclists, nclist_is_q,     maxgap, minoverlap, type, select, circle.length, PACKAGE = "IRanges")
 3: IRanges:::NCList_find_overlaps_in_groups(ranges(query), q_space,     q_groups, ranges(subject), s_space, s_groups, nclists, nclist_is_q,     maxgap, minoverlap, type, select, circle_length)
 4: findOverlaps_GNCList(query, subject, maxgap = maxgap, minoverlap = minoverlap,     type = type, select = "count", ignore.strand = ignore.strand)
 5: .local(query, subject, maxgap, minoverlap, type, ...)
 6: countOverlaps(dj, fragments)
 7: countOverlaps(dj, fragments)
 8: FUN(X[[i]], ...)
 9: lapply(X = X, FUN = FUN, ...)
10: sapply(integer(n), eval.parent(substitute(function(...) expr)),     simplify = simplify)
11: replicate(2, countOverlaps(dj, fragments))

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

> sessionInfo()
R version 3.3.0 Patched (2016-05-20 r70657)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices datasets  utils
[8] methods   base

other attached packages:
[1] GenomicRanges_1.24.2 GenomeInfoDb_1.8.1   IRanges_2.6.1
[4] S4Vectors_0.10.1     BiocGenerics_0.18.0  setwidth_1.0-4
[7] colorout_1.1-1

loaded via a namespace (and not attached):
[1] zlibbioc_1.18.0 XVector_0.12.0  tools_3.3.0