similar to: RSXML - Parsing XML Documents on Internet

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

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 <-

Can't seem to get the code below working. It gets stuck on line 24 inside the function hm; comments show the line in question. The function hm is called by sapply and is at the bottom of the code. Other stuff above line 24 works correctly including the first couple of lines of the function hm. Should I be using a different apply function or am I doing something wrong with xmlTreeParse ?

I would like to track in which journals articles about a particular disease are being published. Creating a pubmed search is trivial. The search provides data but obviously not as an R dataframe. I can get the search to export the data as an xml feed and the xml package seems to be able to read it. xmlTreeParse("

I have a shared partial which could be rendered by two different controllers. Is there an easy way in the view to return which controller rendered the partial? I''ve tried using: <%debug(params[''controller''])%> While that does return what I need it seems like a kludgy fit since debug is not meant to be used for that. Thanks, LarsenMTL -- Posted via

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

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

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!

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

How can I use the try catch block such that if this statement fails xml <- xmlTreeParse(xmlTxt, useInternal=TRUE) then this statement is executed xml <- xmlMalFormed() ? This code does not work but assuming its somewhere along these lines: tryCatch(xml <- xmlTreeParse(xmlTxt, useInternal=TRUE), xml <- xmlMalFormed(f1)) -- View this message in context:

I am trying to read a number of XML files using xmlTreeParse(). Unfortunately, some of them are malformed in a way that makes R crash. The problem is that closing tags are sometimes repeated like this: <tag>value1</tag><tag>value2</tag>some garbage</tag></tag><tag>value3</tag> I want to preprocess the contents of the XML file using gsub() before

Hi! I am trying to install the RMySQL package. The installation stops with the following error message. path to mysql is set. setenv PKG_CPPFLAGS /home/arabidopsis/software/R1.9.1/linux/mysql/include setenv PKG_LIBS /home/arabidopsis/software/R1.9.1/linux/mysql/lib R CMD INSTALL RMySQL_0.5-5.tar.gz #....cut cut. creating src/Makevars ** libs gcc

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,

Dear R-helpers, I have just installed R2.0.0 onto my machine which already had R1.9.1 present. I then tried to add to R2.0.0 a library called GLMM written by James McBroom for R1.6.0. Unfortunately, R2.0.0 does not recognise the library, even though R1.9.1 does. This is not because I have used the wrong case in the call to the library: > library('GLMM') > "Error in

Hallo! I read SPSS data in the following way: library(Hmisc) library(foreign) dat<-spss.get("surv_abb.sav") In R1.9.1 I got the message: "Error in all(arg == choices) : Object "typeDate" not found" In R1.8.0 the same script works fine. Does anybody know a possibilty to read a SPSS file under R1.9.1? Thanks! Karl

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, Why is the following retuning a nodset of length 0: > library(XML) > test <- xmlTreeParse( > "http://www.unimod.org/xml/unimod_tables.xml",useInternalNodes=TRUE) > getNodeSet(test,"//modifications_row") Thanks for any hint. Joh

Full_Name: Sven Sandin Version: 2.0.0 OS: SuSE Linux 9.0 Submission from: (NULL) (81.227.17.135) Have just compiled and installed R-2.0.0.tar.gz running SuSE9.0. The function vcov do not accept "coxph" object as input any longer. The same R-program running R1.9.1 do work. R-program attached below. Exporting the coxph object from R2.0.0 to R1.9.1 I get vcov ouput in R1.9.1. Exporting

Dear All I am doing one distributed data mining program. So I selected GridR package for the distributed programming. *grid.init(service="local",debug=FALSE, localTmpDir="GridRTmp/") grid.apply("x",UCS, wait=TRUE )* UCS is a function. When I execute this statement, I have some errors like : *cannot load local function/variable: xmlRoot extracted from line: : no