Re: [Bioc-sig-seq] scanBam segfault

[Martin Morgan]

On 07/15/2011 02:40 AM, Martin Morgan wrote:
On 07/14/2011 01:11 PM, Ivan Gregoretti wrote:
Hello everybody,
scanBam() is reporting segfaults. I tried in two different machines,
with identical error reports.

The segfault is fixed in Rsamtools 1.5.39; the bug was introduced in 
1.5.35. Thanks for the report.

Martin


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?

I don't have immediate access to HiSeq bam files; are there any publicly
available?

Also, it would help to have a C-level backtrace, maybe by doing

R -d gdb -f test.R

where test.R contains a basic script to reproduce the crash. You'll end
up at the gdb prompt. Type 'r' to run

gdb> r

and then when the segfault occurs

gdb> bt

to generate the back trace (maybe several screens). If you could forward
that to me, on or off list, that would be a better starting point.

Martin

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

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