Hi, Our sysadmin updated libxml2 to version 2.7.8, and now xmlTreeParse works fine with no segfault.
Thank you very much - that was very helpful, Janet On Jun 8, 2011, at 11:59 AM, Janet Young wrote: > Dear Prof Ripley, > > Apologies - I've re-sent that to Duncan Temple Lang, along with your note > about lib versions. > > Version info was included in my original post - I gave full sessionInfo(). > It's XML_3.4-0. > > I only have a very sketchy understanding of libraries and systems > administration, but it looks like our libxml2 is version 2.6.26. I'll ask my > sysadmin people whether they can update that, and try again. > > Janet > > > > On Jun 7, 2011, at 10:54 PM, Prof Brian Ripley wrote: > >> On Tue, 7 Jun 2011, Janet Young wrote: >> >>> Hi, >>> >>> I found an architecture-specific segfault problem with the XML package. I >>> originally found the problem using the parseKGML2Graph function in the >>> Bioconductor KEGGgraph package, but as far as I can tell the underlying >>> issue seems to be with the xmlTreeParse which is called by parseKGML2Graph. >>> >>> I'm trying this piece of code, from the xmlTreeParse help page: >>> >>> library(XML) >>> fileName <- system.file("exampleData", "test.xml", package="XML") >>> x <- xmlTreeParse(fileName) >>> >>> On my Mac and on nodes of one of the linux clusters I have access to, this >>> works fine. But on another of the linux clusters I use, I get a segfault >>> every time, on both 32-bit and 64-bit nodes of the cluster. The unames for >>> those nodes are here: >>> >>> Linux kong053 2.6.18-194.17.1.el5xen #1 SMP Wed Sep 29 13:30:21 EDT 2010 >>> x86_64 x86_64 x86_64 GNU/Linux >>> Linux king049 2.6.18-194.26.1.el5xen #1 SMP Tue Nov 9 14:13:46 EST 2010 >>> i686 i686 i386 GNU/Linux >>> >>> I think I've included all the relevant info below, but please let me know >>> if there's anything else you'd like to see. >> >> As the posting guide says, report problems in contributed packages first to >> the maintainer, giving the 'at a minimum' information required (which >> includes the package version number). >> >> But note that package XML relies on libxml2, and it is entirely possible the >> fault is in the latter. Your kernel looks like RHEL 5 (and is an old >> version): that is well known for having very old versions of system >> software. One known issue with libxml2 is a mismatch between it and zlib >> 1.2.[45] prior to libxml2 2.7.7 (2.7.8 is current): from experience, that >> causes segfaults in package XML's examples. >> >>> >>> thanks, >>> >>> Janet >>> >>> ------------------------------------------------------------------- >>> >>> Dr. Janet Young >>> >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Avenue N., C3-168, >>> P.O. Box 19024, Seattle, WA 98109-1024, USA. >>> >>> tel: (206) 667 1471 fax: (206) 667 6524 >>> email: jayoung ...at... fhcrc.org >>> >>> >>> ------------------------------------------------------------------- >>> >>> >>> >>> >>> >>> >>> ######## on 64-bit node >>> >>>> library(XML) >>> >>>> fileName <- system.file("exampleData", "test.xml", package="XML") >>> >>>> fileName >>> [1] "/home/btrask/traskdata/lib_linux_64/R/library/XML/exampleData/test.xml" >>> >>>> sessionInfo() >>> R version 2.13.0 (2011-04-13) >>> 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=C 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] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] XML_3.4-0 >>> >>> >>>> system("uname -a") >>> Linux kong053 2.6.18-194.17.1.el5xen #1 SMP Wed Sep 29 13:30:21 EDT 2010 >>> x86_64 x86_64 x86_64 GNU/Linux >>> >>>> x <- xmlTreeParse(fileName) >>> >>> *** caught segfault *** >>> address 0x500001c4f, cause 'memory not mapped' >>> >>> Traceback: >>> 1: .Call("RS_XML_ParseTree", as.character(file), handlers, >>> as.logical(ignoreBlanks), as.logical(replaceEntities), >>> as.logical(asText), as.logical(trim), as.logical(validate), >>> as.logical(getDTD), as.logical(isURL), >>> as.logical(addAttributeNamespaces), as.logical(useInternalNodes), >>> FALSE, as.logical(isSchema), as.logical(fullNamespaceInfo), >>> as.character(encoding), as.logical(useDotNames), xinclude, error, >>> addFinalizer, PACKAGE = "XML") >>> 2: xmlTreeParse(fileName) >>> >>> Possible actions: >>> 1: abort (with core dump, if enabled) >>> 2: normal R exit >>> 3: exit R without saving workspace >>> 4: exit R saving workspace >>> Selection: >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >> >> -- >> Brian D. Ripley, rip...@stats.ox.ac.uk >> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ >> University of Oxford, Tel: +44 1865 272861 (self) >> 1 South Parks Road, +44 1865 272866 (PA) >> Oxford OX1 3TG, UK Fax: +44 1865 272595 > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.