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:
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--
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.
