[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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>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
>


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