search for: xmleventparse

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 <spectrum id="2">, <mzArrayBinary>, <intenArrayBinary> <... name="MassToChargeRatio" value...

...r the <anonymous> label, and I get something like this: $by.total total.time total.pct self.time self.pct "system.time" 151.22 99.99 0.00 0.00 "MyParsingFunction" 149.38 98.77 0.00 0.00 "xmlEventParse" 149.38 98.77 0.00 0.00 ".Call" 149.32 98.73 3.04 2.01 "<Anonymous>" 146.74 97.02 141.26 93.40 <--- !! "xmlValue" 3.04 2.01 0.46...

...lRM_PA_CY_SL_Fig) 46 : term verbatim(label=IPClassDistRelRM_PA_CY_SP_Fig) 47 : term xml(label=IPTrans_TS_SL_count) 48 :(label=IPTrans_TS_SP_count) 49 : term verbatim(label=close) 'content_1.xml' has been Sweaved Removing content.xml Post-processing the contents Error in xmlEventParse(infile, handlers = handlers, trim = FALSE, state = state) : attempt to apply non-function In addition: Warning message: closing unused connection 3 (content.xml) > --------------------------------------------------------------- -- "Life is like a trumpet - if you don't put anythi...

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

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 parsing after the first umlaut an...

...-DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -c XMLEventParse.c -o XMLEventParse.o In file included from XMLEventParse.c:5: Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" XMLEventParse.c: In function ?R_processBranch?: XMLEventParse.c:349: warning: initialization from incompatible pointer type gcc -...

...Now I want to extract only node 'pubdate' and its children, but I don't know how to do that unless I try to dig into the structure of the XML file. The problem is that structure can differ and then hardcoded set of list indices i.e. tmp[[i]][[j]]... doesn't help me. I've read xmlEventParse but I don't understand handlers part up to the point that I could get anything usable from it. Here is something not very usable ;) PubDate <- function(x, ...) { print(x) } xmlEventParse(URL, isURL = TRUE, handlers=list(PubDate=PubDate), addConte...

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> - <Data> - <dataSets noOfDataSets="50000"> - <dataSet number="1"> - <measurements> - <measurement number="1"> - <MRType1&gt...

...the the three PubDate elements in the document. > >If you wanted both PubDate and PubMedPubDate elements, >you could use > > myHandlers = getElements(c("PubDate", "PubMedPubDate") > >[Note that XML is case-sensitive and pubdate won't work.] > >The xmlEventParse is quite a bit more work as it is for >very low-level parsing, working at the parser level >of opening and closing XML elements. > >The xmlTreeParse is a hybrid parser. It works at the higher >level of nodes, but provides an opportunity to process >nodes when they are "create...

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....

...NCDIR=/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 RSDTD.o RUtils.o Utils.o XMLEventParse.o XMLTree.o -lz -lxml2 ld: multiple definitions of symbol _xmlParserError Utils.o definition of _xmlParserError in section (__TEXT,__text) /usr/local/lib/libxml2.dylib(libxml2.2.5.9.dylib-master.o) definition of _xmlParserError make: *** [XML.so] Error 1 ERROR: compilation failed for package '...

...URN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -O2 -pipe -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -c XMLEventParse.c -o XMLEventParse.o In file included from XMLEventParse.c:5:0: Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp] XMLEventParse.c: In function 'R_processBranch': XMLEventParse.c:351:20: warning: initialization from incompatib...

...ibxml -DLIBXML -I/sw/include/gnome-xml Link flags: -L/sw/lib -lxml -lz -lz -lxml Compiling produced the following error: gcc -bundle -flat_namespace -undefined suppress -L/sw/lib -L/usr/local/lib -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o RSDTD.o RUtils.o Utils.o XMLEventParse.o XMLTree.o -L/sw/lib -lxml -lz -lz -lxml -lcc_dynamic ld: multiple definitions of symbol _xmlParserError Utils.o definition of _xmlParserError in section (__TEXT,__text) /sw/lib/libxml.dylib(error.lo) definition of _xmlParserError make: *** [XML.so] Error 1 ERROR: compilation failed for package...

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",

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

Dear all I am trying to use the ODB package to connect to an libreoffice-odb database. The libreoffice package is german, thus, decimal separator is a comma. However, I can open the database and upload a it without error, library(ODB) db <- odb.open("Test.odb") but a soon as the "odb.open" command is executed, the decimal separator in R is changed to comma. Before