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'
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]]
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 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.-- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
xmlDoc() is not the function to use to parse a file.
Use
doc = xmlParse("Malaria_Grave.xml")
xmlDoc() is for programmatically creating a new XML within R.
It could be more robust to being called with a string, but
the key thing here is that it is not the appropriate function for what
you want.
Also, if there had been a problem with the parsing, you'd need to give
me/us the offending XML file so that we could have a chance of reproducing
the problem.
D.
On 8/24/10 2:35 PM, 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'
>
> 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 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.