[Bioc-devel] scanBam() segfault error

On 04/17/2015 09:12 AM, Martin Morgan wrote:

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

Thanks Leonard, I think this is addressed in 1.20.1 / 1.21.1, which are not
yet available via biocLite.

I will likely revisit this code in the next week or so; please let me know
if there are other issues.


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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