similar to: SAX Parser best practise

Hello everyone, I'm trying to parse a very large XML file using SAX with the XML package (i.e., mainly the xmlEventParsing function). This function takes as an argument a list of other functions (handlers) that will be called to handle particular xml nodes. If when I use Rprof(), all the handler functions are lumped together under the <anonymous> label, and I get something like this:

Hello! I am trying to get specific fields from an XML document and I am totally puzzled. I hope someone can help me. # URL URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation" # download a XML file tmp <- xmlTreeParse(URL, isURL = TRUE) tmp <- xmlRoot(tmp) Now I want to extract only

Dear all, for my diploma thesis I have to import huge XML-Files into R for statistical processing - huge means a size about 33 MB. I'm using the XML-Package version 1.9 As far as reading the complete file into R via xmlTreeParse doesn't work or is too slow, I'm trying to use xmlEventParse but I got completely stuck. I have many different type of nodes + <configuration>

Hi all, thanks to the people who replied to my question! I finally solved the issue by writing own handlers and using xmlEventParse - which leads to the following problem which is so odd that its probably a bug. I use several special charachter in my XML-File, e.g. umlauts or ? or ? - but no matter how I encode my XML (UTF or ISO) or I escape these characters xmlEventParse always stops

Hello everyone, I am probably not the only one having trouble with this package but here goes. I want to install XML on Ubuntu. I installed libxml2-dev and everything works out fine until I get the following: Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, : No definition was found for superclass "namedList" in the specification of class

Duncan, you are a king! Thanks a lot for this cookie. It really helped me. Thanks for the code as well as detailed explanation at the end. >Hi Gregor. > >Here is a function that will collect all of the nodes in the >XML document whose names are in the vector elementNames > >getElements = >function(elementNames) >{ > els = list() > > startElement = function(node,

I am getting the following error when using odfWeave Error in xmlEventParse(infile, handlers = handlers, trim = FALSE, state = state) : File content_1.xml does not exist This appears to be the same issue detailed in http://markmail.org/message/qsrqdtozizlngbrt#query:+page:1+mid:qsrqdtozizlngbrt+state:results however the link to XML_1.93-2.3.zip appears to be dead. Is there either a better

I am working to build the XML package for R on MacOS X. I have installed libxml2-2.5.9 into /usr/local. I set the LIBXML_INCDIR=/usr/local/include/libxml2. I use R INSTALL, I get the following: R INSTALL -c -l /usr/local/R/library XML_0.94-1.tar.gz : : : gcc -bundle -flat_namespace -undefined suppress -L/sw/lib -L/usr/local/lib -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o

I am trying to build the XML package on MacOS. I am using the fink installation of libxml-1.8.17. The configuration information is: Configuration information: Libxml settings libxml include directory: /sw/include/gnome-xml libxml library directory: -L/sw/lib -lxml -lz -lz -lxml libxml 2: no Compilation flags: -I/sw/include/gnome-xml -I/sw/include/gnome-xml/libxml

Could someone provide a link or examples of parsing XML document in R? Few specific questions below: For instance I can retrieve specific nodes using this: node <- xpathApply(xml, "//" %+% xtag, xmlValue) 1) I want to be able to retrieve parent node for this node, how can I do this? getParentNode() does not seem to cut it. 2) How can I retrieve children nodes for a particular

odfWeave is throwing up a cryptic error, after successfully processing a file with a large number of figures (~30) and many \Sexpr{} calls. The error is (at least to me) cryptic. I am not sure where to look to correct this problem. Here's the error: Post-processing the contents Error in .Call("RS_XML_Parse", file, handlers, endElementHandlers, as.logical(addContext), :

Hello again, I have another question related to parsing a very large xml file with SAX: what kind of data structure should I favor? Unlike using DOM function that can return lists of relevant nodes and let me use various versions of 'apply', the SAX parsing returns me one thing at a time. I first tried to simply append to simple solution of appending to lists as I get the data. But I

CentOS Errata and Bugfix Advisory 2012:1184 Upstream details at : http://rhn.redhat.com/errata/RHBA-2012-1184.html The following updated files have been uploaded and are currently syncing to the mirrors: ( sha256sum Filename ) i386: 85aed94f1ee9a2c4886d2bbca6ccd73b59d9e9e0903f866c84e12219703faeca perl-XML-SAX-0.14-13.el5.noarch.rpm x86_64:

CentOS Errata and Bugfix Advisory 2011:1446 Upstream details at : http://rhn.redhat.com/errata/RHBA-2011-1446.html The following updated files have been uploaded and are currently syncing to the mirrors: ( md5sum Filename ) i386: 47eeab4c308fbf62d697aa7130cad9a4 perl-XML-SAX-0.14-11.noarch.rpm Source: 87dceb01f600717c787f9bc069d5bac9 perl-XML-SAX-0.14-11.src.rpm -- Johnny Hughes CentOS

CentOS Errata and Bugfix Advisory 2011:1446 Upstream details at : http://rhn.redhat.com/errata/RHBA-2011-1446.html The following updated files have been uploaded and are currently syncing to the mirrors: ( md5sum Filename ) x86_64: 47eeab4c308fbf62d697aa7130cad9a4 perl-XML-SAX-0.14-11.noarch.rpm Source: 87dceb01f600717c787f9bc069d5bac9 perl-XML-SAX-0.14-11.src.rpm -- Johnny Hughes

Hi, I''m trying to parse a XML document and put some of that information inside a rhtml file. I also have partials that I want to wrap around content in the XML stream. However, I don''t have any clue how to pass an object to the SAX2Listener so it can combine the partials and the XML together. Normally, in java I would pass the HttpResponse object or the PrintWriter

Hi, I have mentioned before that we have added some sdt dtrace probes in SAX, our APL interpreter. Encouraged by Angelo and Jignesh, I have created a small document (5 pages) describing our experience with it, together with some problems we have encountered and some scripts we use for pretty-printing dtrace outputs. The said document can be found at

I tried to build (and install) XML_3.95-0.1.tar.gz on FreeBSD 10.0-CURRENT amd64, but it stopped during the check of R_HAS_REMOVE_FINALIZERS (full log appended): ---------------------------------- R CMD INSTALL XML_3.95-0.1.tar.gz [..snip..] Checking for 1.8: -DR_HAS_REMOVE_FINALIZERS=1 -I/usr/local/include/libxml2 -I/usr/local/include Using libxml2.* checking for gzopen in -lz... gcc46

Dear list, Sorry for bothering you with a pure odfSweave question, but I just ran into a problem that I cannot find the cause of. Anyonse seen this before? This file "used to work", but not anymore. Would apreciate all the help I could get. /Fredrik --------------------------------------------------------------- >

hello all, I trying to use the package 'odfWeave' and I get the follow error: ### error message ############################################################# ... Removing content.xml Post-processing the contents Error in .Call("RS_XML_Parse", file, handlers, as.logical(addContext), : Error in the XML event driven parser for content_1.xml: error parsing attribute name