It seems to be a bug on the XML package.
This is what I run (and it is not the only file):
> library("XML")
> doc <- xmlDoc("Malaria_Grave.xml")
*** caught segfault ***
address 0x9, cause 'memory not mapped'
Traceback:
1: .Call("RS_XML_createDocFromNode", node, PACKAGE = "XML")
2: xmlDoc("Malaria_Grave.xml")
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: 1
aborting ...
Segmentation fault
##=========================
> sessionInfo()
R version 2.11.1 (2010-05-31)
i686-pc-linux-gnu
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_3.1-1
>
##=========================
Thanks
Caveman
On Wed, Aug 25, 2010 at 12:02 AM, Gavin Simpson <gavin.simp...@ucl.ac.uk>wrote:
> On Tue, 2010-08-24 at 23:35 +0200, Orvalho Augusto wrote:
> > I have one XML file with 30MB that I need to read the data.
> >
> > I try this;
> > library(XML)
> > doc <- xmlDoc("Malaria_Grave.xml")
> >
> > And R answers like this
> > *** caught segfault ***
> > address 0x5, cause 'memory not mapped'
>
> This is most likely a bug in your version (unstated) of the XML package.
> But it may be a problem with the file, though XML shouldn't crash R.
> Make sure you are using the latest version of the XML package and R is
> up-to-date, then retry your code in a new R session. If it still
> segfaults, you need to file a bug report with the maintainer: Duncan
> Temple Lang, and include all the relevant details such as output from
>
> sessionInfo()
>
> The .xml file you are trying to read and the code required to reproduce
> the segfault.
>
> HTH
>
> G
>
> > Traceback:
> > 1: .Call("RS_XML_createDocFromNode", node, PACKAGE = "XML")
> > 2: xmlDoc("Malaria_Grave.xml")
> >
> > Possible actions:
> > 1: abort (with core dump, if enabled)
> > 2: normal R exit
> > 3: exit R without saving workspace
> > 4: exit R saving workspace
> >
> >
> > Or I try this:
> > doc <- xmlTreeParse("Malaria_Grave.xml")
> >
> > I get this
> > xmlParseEntityRef: no name
> > xmlParseEntityRef: no name
> > Error: 1: xmlParseEntityRef: no name
> > 2: xmlParseEntityRef: no name
> >
> > Please guys help this simple mortal!
> > Caveman
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > 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.
>
> --
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> Dr. Gavin Simpson [t] +44 (0)20 7679 0522
> ECRC, UCL Geography, [f] +44 (0)20 7679 0565
> Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
> Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
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>
>
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