[BioC] rsamtools scanBcf segfault

[Rob Syme]

Hi all,
I'm looking to read in a bcf file, but R keeps segfaulting out. I'd
love advice or pointers if anyone has seen this before.
Environment:
Rsamtools version 1.4.2
R version 2.13.1 (2011-07-08)

Code to reproduce is gist.github.com/1109210, reproduced below:

wget https://gist.github.com/raw/1109207/8a3cd8a8801e96f67865f8a35ca6608ae7fe9927/subset.vcf
grep -v "^#" subset.vcf | cut -f 1  | sort -u > subset.dict
bcftools view -D subset.dict -bS subset.vcf > subset.bcf
bcftools index subset.bcf
wget https://gist.github.com/raw/1109213/a325d29ee4cfa7f2c7107d085ed813cdd942c083/segfault.R
Rscript segfault.R
## END BASH
I get:

$ Rscript segfault.R
...
 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: .Call(func, .extptr(file), space, tmpl)
 2: doTryCatch(return(expr), name, parentenv, handler)
 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 4: tryCatchList(expr, classes, parentenv, handlers)
 5: tryCatch({    .Call(func, .extptr(file), space, tmpl)}, error =
function(err) {    stop("scanBcf: ", conditionMessage(err), "\n  path:
", path(file),         call. = FALSE)})
 6: .io_bcf(.scan_bcf, file, ..., param = param)
 7: .local(file, ...)
 8: scanBcf(bcf, param = param)
 9: scanBcf(bcf, param = param)
aborting ...
Segmentation fault