My system is an Ubuntu 9.10 32bit: #uname -a Linux cavemanpc 2.6.31-22-generic #63-Ubuntu SMP Wed Aug 18 22:54:26 UTC 2010 i686 GNU/Linux
# free -m total used free shared buffers cached Mem: 3000 1847 1152 0 120 961 -/+ buffers/cache: 766 2234 Swap: 4769 0 4769 My Ubuntu XML related packages: r...@cavemanpc:~# dpkg -l | grep -i libxml | awk '{ print $2}' libxml++2.6-2 libxml++2.6-dev libxml-commons-external-java libxml-commons-resolver1.1-java libxml-java-openoffice.org libxml-parser-perl libxml-twig-perl libxml-xpath-perl libxml2 libxml2-dev libxml2-utils libxmlgraphics-commons-java python-libxml2 Thanks Caveman On Wed, Aug 25, 2010 at 12:43 AM, Orvalho Augusto <orvaq...@gmail.com>wrote: > 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. >> >> -- >> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% >> 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 >> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% >> >> > > > > [[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.