similar to: Parsing very large xml datafiles with SAX: How to profile <anonymous> functions?

Dear All, I have a question regarding best practise in setting up a XML parser within R. Because I have files with more than 100 MB and I'm only interested in some values I think a SAX-like parser using xmlEventParse() will be the best solution. Unfortunately the values I'm looking for, to construct some higher "mass spectrum", are distributed over different lines: as

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>

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

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

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,

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

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

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

Hi, Consider the following code: require(XML) xmlFile = paste( "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n", "<mzXML xmlns=\"a\" xmlns:xsi=\"b\" xsi:schemaLocation=\"c\">\n", "<parentFile a=\"a\" b=\"b\" />\n",

Dear, I want to read XML documents, add child nodes to some elements and store everything back as an XML document. I've tryed the following: doc <- xmlTreeParse("file.xml") QTListNode<-xmlElementsByTagName(xmlRoot(doc)[[1]],"tagname") append.xmlNode(QTListNode[[1]],newXMLNode(name ="Norm", attrs = NULL)) saveXML(doc, file = "out.xml",

This message is about a curious difference in timing between two ways of computing the same function. One uses expm, so is expected to be a bit slower, but "a bit" turned out to be a factor of >1000. The code is below. We would be grateful if anyone can point out any egregious bad practice in our code, or enlighten us on why one approach is so much slower than the other. The problem

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

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

Hola, muy buenas, Me bajé un archivo xml de la wikipedia en español. Al intentar abrirlo en R el ordenador no es capaz, ya que pesa descomprimido 10 GB. De ese xml solo me interesa un campo, el referente al texto del artículo. ¿Alguiém conoce alguna forma de cargar solo ese campo del xml en R sin cargar el xml completo? La salida seria un archivo .txt, donde cada fila fuera un artículo ó

Hello I'm trying to register an Asterisk working behind Nat. Here is the trunk: register=username:password at sip.startel.pt [startel] type=peer host=sip.startel.pt username=username fromuser=username secret=password qualify=yes disallow=all allow=ulaw allow=alaw allow=gsm insecure=very port=5060 nat=yes canreinvite=yes The problem is: Asterisk is registering with its