[BioC] rsamtools scanBcf segfault

[Martin Morgan]

On 07/27/2011 05:17 AM, Rob Syme wrote:
> 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:

Thanks Rob for the nice reproducible example. The problem is when you 
open the BcfFile; 'mode' should be 'rb' to indicate that you want to 
read a binary file. Or leave it unspecified and the heuristic will do 
the right thing.

I'll try to get a fix in so that R doesn't seg fault.

Martin

>
> $ 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
>
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