[Bioc-devel] scanBam() segfault error

[Martin Morgan]

On 04/17/2015 08:59 AM, Leonard Goldstein wrote:
> Hi all,
>
> I ran into a segfault error when trying to read paired-end RNA-seq
> alignments with scanBam (see below). This seems to be a problem
> introduced in Rsamtools version 1.19.35 (1.19.34 works fine). In case
> you need the BAM file for testing, please let me know. Many thanks for

Probably a BAM file would be a big help... Thanks, Martin

> your help.
>
> Leonard
>
>
>> sessionInfo()
> R Under development (unstable) (2014-11-04 r66932)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> 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] parallel  stats4    stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] Rsamtools_1.19.54     Biostrings_2.35.13    XVector_0.7.4
> [4] GenomicRanges_1.19.57 GenomeInfoDb_1.3.20   IRanges_2.1.45
> [7] S4Vectors_0.5.23      BiocGenerics_0.13.11
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-6    compiler_3.2.0  tools_3.2.0     zlibbioc_1.13.3
>>
>> gr <- GRanges("16", IRanges(13173149, 15234449), "+")
>>
>> file <- BamFile(file, asMates = TRUE)
>>
>> param <- ScanBamParam(what = scanBamWhat(), which = gr)
>>
>> tmp <- scanBam(file = file, param = param)
>
>   *** caught segfault ***
> address 0x14538b1e, cause 'memory not mapped'
>
> Traceback:
>   1: .Call(func, .extptr(file), space, flag, simpleCigar, tagFilter,     ...)
>   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, flag, simpleCigar,
> tagFilter,         ...)}, error = function(err) {
> stop(conditionMessage(err), "\n  f\
> ile: ", path(file), "\n  index: ",         index(file))})
>   6: .io_bam(.scan_bamfile, file, reverseComplement, yieldSize(file),
>    tmpl, obeyQname(file), asMates(file), qnamePrefix, qnameSuffix,
> param = param)
>   7: scanBam(file = file, param = param)
>   8: scanBam(file = file, param = param)
>
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


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