similar to: GridR

R Users: After installing Bioconductor, RSXML and all the relevant Win32 DLLs (libxml2, zlib, iconv), I receive the following error message when using pm.getabst() Error in xmlRoot(absts) : no applicable method for "xmlRoot" I receive this when using the example from help(pm.getabst). Downloading the target XML file, parsing it with xmlTreeParse and applying xmlRoot returns no

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",

Hi, I'm trying to use the XML package to read an RSS feed. To get started, I was trying to use this post as an example: http://www.r-bloggers.com/how-to-build-a-dataset-in-r-using-an-rss-feed-or-web-page/ I can replicate the beginning section of the post, but when I try to use another RSS feed I have an issue. The RSS feed I would like to use is: > URL <-

Is there any function to write a XML structure, after it was read using xmlTreeParse? Ex: library(XML) x <- xmlTreeParse("Irpf2008/aplicacao/dados/12345678901/12345678901.xml") # write it... Alberto Monteiro PS: please, brazilians, don't be offended by my foul language!

Hello all, I have a problem with the way attributes are dealt with in the function xmlToList(), and I haven't been able to figure it out for days now. Say I have a document (produced by nmap) like this: > mydoc <- '<host starttime="1365204834" endtime="1365205860"><status state="up" reason="echo-reply"

Hello again, Another stumble here that is defeating me. I try: a<-readLines(url("http://feeds.feedburner.com/grokin")) t<-XML::xmlTreeParse(a, ignoreBlanks=TRUE, replaceEntities=FALSE, asText=TRUE) elem<- XML::getNodeSet(XML::xmlRoot(t),"/rss/channel/item")[[1]] And I get: Start tag expected, '<' not found Error: 1: Start tag expected, '<' not

Hi all, this is my first post in this mailing group. I hope that anyboby could help me parsing a xml file. I found this website http://www.omegahat.org/RSXML/gettingStarted.html but unfortunately my XML file is not as easy as the one in the example. Example: <?xml version="1.0" encoding="UTF-8"?> <?xml-stylesheet

I'm struggling with package XML to parse a Garmin file (named *.tcx). I wonder if it's form is incomplete, but appreciably reluctant to paste even a shortened version. The output below shows I can get nodes, but an attempt at value of a single node comes up empty (even though there is data there. One question: Has anybody succeeded parsing Garmin .tcx (xml) files? Thanks! Michael

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 useRs, I have a simple/RTFM question about XML parsing. Given an XML file, such as (fragment) <A>100</A> <B>23</B> <C>true</C> how do I import it in a data frame or list, so that the values (100, 23, true) can be accessed through the names A, B and C? I installed the XML package and looked over the documentation... however after 20 minutes and a couple of

Hi, I have an existing XML document on disk, which I'd like to use as a template, and exchange a subnode with my own newly created subtree: <?xml version="1.0"?> <Duncan> <name a="1" b="xyz"> <first>Duncan</first> <last>Temple Lang</last> </name> </Duncan> created by e.g. ? library(XML)

Hello dear R-help group (and David Smith from REvolution), I would like to perform parallel computing using R with Condor (hopefully using foreach or other recommended solutions, if available) for some "Embarrassingly parallel" problem. I will start by listing what I found so far, and then go on asking for help. So far I found the a manual by Xianhong Xie from Rnews_2005-2 (see page

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'm attempting to read information from an XML into a data frame in R using the "XML" package. I am unable to get the data into a data frame as I would like. I have some sample code below. *XML Code:* Header... Data I want in a data frame: <data> <row BRAND="GMC" NUM="1" YEAR="1999" VALUE="10000" /> <row

Hi, I am trying to use 'GridR' package for the first time, and I'm running into a strange error from grid.check: > grid.check(gridFun) Error in exists(add) : invalid first argument After playing around in recover mode, I see that this because the variable 'add' created by grid.check is blank: Browse[1]> split[[1]][k] [1] " : " Browse[1]> add [1]

Dear all I am implement one grid computing system using GridR package. I am working on windows platform. I did all the configuration according to the GridR tutorial. But it has some errors when I execute grid.apply function. Here is the output from stderr: R: not found java.io.IOException: Error during SCP transfer. at com.trilead.ssh2.SCPClient.get(SCPClient.java:703) at

Hello! I am not experienced enough to know whether I have found a bug or whether I am just ignorant. I have been trying to use the tm package to read in material from RSS 2.0 feeds, which has required grappling with writing a reader for that flavour of XML. I get an error - "Error : 1: EntityRef: expecting ';' - which I think I've tracked down. The feed being processed is from

Hello! I am crossposting this to R-help and BioC, since it is relevant to both groups. I wrote a wrapper for Entrez search utility (link for this is provided bellow), which can add some new search functionality to existing code in Bioconductor's package 'annotate'*. http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Entrez search utuility returns a XML document

Hi, I found an architecture-specific segfault problem with the XML package. I originally found the problem using the parseKGML2Graph function in the Bioconductor KEGGgraph package, but as far as I can tell the underlying issue seems to be with the xmlTreeParse which is called by parseKGML2Graph. I'm trying this piece of code, from the xmlTreeParse help page: library(XML) fileName <-

Hi, I have a problem with spacing in XML files when reading them with xmlTreeParse. I don't know the exact specification of xml but according what I have red before it should work. consider a tiny test.xml file: <?xml version="1.0"?> <fields> <v1>1 </v1> <v2> 2 </v2> <v3> 3</v3> </fields> i.e. I have three fields v1, v2 and