[Bioc-sig-seq] scanBam segfault

[Ivan Gregoretti]

Hello everybody,

scanBam() is reporting segfaults. I tried in two different machines,
with identical error reports.

Actually, I have four BAM files from which I am only reading in the
oligo sequences, nothing else. Two of them load fine but the other two
produce the error.

Loading fine: BAMs with 70887462 and 58162986 records
Loading with segfault: BAMs with 101611824 and 114530023

So, smaller are fine, bigger just crash.

Do you guys run into the same problem?

Thank you,

Ivan

*****************************************************************

> filebam  <- "/home/igregore/my/data3/runs/110705/Project_81BRRABXX/c466.bam"
> filebai  <- "/home/igregore/my/data3/runs/110705/Project_81BRRABXX/c466"
> param    <- ScanBamParam(what = c("seq"))
> myheader <- scanBamHeader(file=filebam)
> c466Ba <- scanBam(file=filebam, index=filebai, param=param)

 *** caught segfault ***
address 0x7fb9a9773030, cause 'memory not mapped'

Traceback:
 1: .Call(func, .extptr(file), space, flag, simpleCigar, ...)
 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,
...)}, error = function(err) {    stop(conditionMessage(err), "\n
file: ", path(file), "\n  index: ",         index(file))})
 6: .io_bam(.scan_bamfile, file, param = param, path(file),
index(file),     "rb", reverseComplement, tmpl)
 7: scanBam(bam, param = param)
 8: scanBam(bam, param = param)
 9: eval(expr, envir, enclos)
10: eval(call, sys.frame(sys.parent()))
11: callGeneric(bam, ..., param = param)
12: scanBam(file = filebam, index = filebai, param = param)
13: scanBam(file = filebam, index = filebai, param = param)

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 2.14.0 Under development (unstable) (2011-04-14 r55450)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

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

other attached packages:
[1] ShortRead_1.11.26    latticeExtra_0.6-18  RColorBrewer_1.0-5
[4] lattice_0.19-30      Rsamtools_1.5.38     Biostrings_2.21.6
[7] GenomicRanges_1.5.16 IRanges_1.11.11

loaded via a namespace (and not attached):
[1] Biobase_2.13.7 grid_2.14.0    hwriter_1.3    zlibbioc_0.1.7