Thank you. Ivan
On Sat, Jul 16, 2011 at 9:20 AM, Martin Morgan <mtmor...@fhcrc.org> wrote: > 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 >>> >>> _______________________________________________ >>> Bioc-sig-sequencing mailing list >>> Bioc-sig-sequencing@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> >> > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing