[R] XML segfault on some architectures

[Janet Young]

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 at 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,                  ripley at 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