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.
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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