similar to: question about XML (package)

Hi everybody, I am using gzipped files quite extensively and cannot figure out how I can close (or reuse) connections. Example: > for(i in 1:300) {cat(i, "\n"); a <- readLines(gzfile("file.gz"), n=1) } 1 2 ... 46 47 Error in gzfile("~/tyyq/andmebaasiq/ETU/ETU1997.tsv.gz") : all connections are in use To use just gzfile without any open/close should

Full_Name: Ott Toomet Version: 2.6.0, 2.5.x OS: debian etch, lenny Submission from: (NULL) (80.235.63.243) When building a package with 'R CMD build name_of_directory" using "et_EE.UTF-8" locale, I get the following: siim at tancredi:~/tyyq/econ/micEcon$ R CMD build trunk * checking for file 'trunk/DESCRIPTION' ... OK * preparing 'trunk': * checking

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

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 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 <-

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:

R Users - I asked about this a few months ago and never did quite figure it out, so with more information, allow me to try again. If I use the following code: library(xml) xmlTreeParse("http://home.comcast.net/~larsenmtl/xmlTestDoc.xml", isURL = TRUE) I receive this error: Error in xmlTreeParse("http://home.comcast.net/~larsenmtl/xmlTestDoc.xml"", : error in

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

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 ?

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

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

Hi, I have an RH9 box (gcc (GCC) 3.2.2, perl 5.8.0, make 3.79.1). My locale is LANG="et_EE.UTF-8" I do: $ ./configure --prefix=/usr/local ... $ make ... make[4]: Entering directory `/home/otoomet/a/R-1.9.0/src/library/stats4' dumping R code in package 'stats4' Error in structure(c(unlist(lapply(list(...), unclass))), class = c("POSIXt", : couldn't

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"

Dear list I tried to read an xml file using the xml package. Unfortunately, some encoding problems occure. E.g. german Umlaut will be red correctly. I assume that the occurs due to (internal?) conversion to utf-8. To illustrate the problem, I have wrote to xml files. File Test 1 ----------- <?xml version="1.0" encoding="ISO-8859-1"?> <Daten> <ITEM>

Hi, are there any function to plot the empirical probability distribution function? I just don't want to reinvent the wheel... Best wishes, Ott -- Ott Toomet PhD Student Dept. of Economics ?rhus University Building 322 Universitetsparken 8000 ?rhus C Denmark otoomet (a) econ au dk ph: (+45) 89 42 20 27 ------------------------------------------- (o_ (*_ (O_

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("

Hi, I have an XML file which contains among other nodes : ===myXMLfile.xml=== (?) <nbRelations>2</nbRelations> <nbActors>2</nbActors> (...) <nbRuns>5</nbRuns> <nbStep>2000</nbStep> (?) ===End file=== I need to extract those values and to make them R variables such as: nbRelations = 2 nbActors = 2 nbRuns = 5 nbSteps = 2000 I read the help and have

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",

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