similar to: Treatment of xml-stylesheet processing instructions in XML module

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

Hello, I'm trying to install KEGGSOAP with bioconductor but i'm facing this problem: /> biocLite("KEGGSOAP") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.4. Installing package(s) 'KEGGSOAP' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/KEGGSOAP_1.30.0.tar.gz' Content type

I am using htmlParse from XML library on a paricular website. Sometimes code fails, sometimes it works, most of the time id doesn't and i cannot see why. The file i am trying to parse is  http://www.londonstockexchange.com/exchange/prices-and-markets/international-markets/indices/home/sp-500.html?page=0 Sometimes the following code works n<-readHTMLTable(htmlParse(url)) But most of the

Dear colleagues, Could I get some assistance using postForm() to scrape the business names and addresses at this website: http://www.brantford.ca/business/LocalBusinessCommunity/Pages/BusinessDirectorySearch.aspx I've read through (http://www.omegahat.org/RCurl/RCurlJSS.pdf) and scoured the web for tutorials, but I can't crack it. I'm aware that this is probably a pretty basic

I am looking for the syntax to capture XML tags marked with /DescriptorName MajorTopicYN="Y"/ , but the combination of the internal space (between "Name" and "Major" and the embedded quote marks are defeating me. I can get all the "DescriptorName" tags, but these include both MajroTopicYN = "Y" and "N" variants. Any suggestions?

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 <-

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 <-

Hello, I am trying to use XML package to download Facebook reviews in the following way: require(XML) mydata.vectors <- character(0) Qword <- URLencode('#IBM') QUERY <- paste('SELECT review_id, message, rating from review where message LIKE %',Qword,'%',sep='') Facebook_url = paste('https://api.facebook.com/method/fql.query?query=

Hi Can some one please point out where i am wrong. I am trying to position set of nodes column-wise in cytoscape using RCytoscape A----D B----E C----F ------------------- g <- new ('graphNEL', edgemode='undirected') cw <- CytoscapeWindow ('smallExample', graph=RCytoscape::makeSimpleGraph()) layout (cw, 'jgraph-spring') redraw(cw) nodesFr = c('A',

Hi all: I struggle a lot scraping web data. I still haven't got a handle on the XML package. I'd like to get particular exchange rates from this table: https://raw.github.com/currencybot/open-exchange-rates/master/latest.json This is the code that I'm working with: library(RCurl) library(XML)

Hello everyone, I would like to parse very large xml files from MS/MS experiments and create R objects from their content. (By very large, I mean going up to 5-10Gb, although I am using a 'small' 40M file to test my code.) My first attempt at parsing the 40M file, using the XML package, took more than 2200 seconds and left me quite disappointed. I managed to cut that down to around 40

This is a question about how to calculate similarities/distances among items that are classified by hierarchical attributes for the purpose of visualizing the relations among items by means of clustering, MDS, self-organizing maps, and so forth. I have a set of ~260 items that have been classified using two sets of hierarchically-organized codes on the basis of form and content. The data looks

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

Dear Lists, Here are my latest posts on retrenching and locating facilities better. Do you have anything in academic papers that use data mining- analytics for 1) Better Employee ROI quantitative measurement or cutting costs rationally based on data rather across the board. 2) Locating facilities based on pure quant based approaches than local supply demand conditions. Specific application for

Hi, I'm looking for help extracting some information of the zillow website. I'd like to do this for the general case where I manually change the address by modifying the url (see code below). With the url containing the address, I'd like to be able to extract the same information each time. The specific information I'd like to be able to extract includes the homedetails url, price

Hey, I have an double loop like this: chunk <- list(1:10, 11:20, 21:30) for(k in 1:length(chunk)){ print(chunk[k]) DummyCatcher <- NULL for(i in chunk[k]){ print("i load something") dummy <- 1 print("i do something") dummy <- dummy + 1 print("i do put it together") DummyCatcher = rbind(DummyCatcher, dummy) } print("i save a chunk

I deal with a huge amount of Biology data stored in different databases. The databases belongig to Bioconductor organization can be accessed through Bioconductor packages. Unluckily some useful data is stored in databases like, for instance, miRDB, miRecords, etc ... which offer just an interactive HTML interface. See for instance http://mirdb.org/cgi-bin/search.cgi,

Hi there, does anybody know how to return the xmlPath from a node? For example, at several location in the xml file, I have nodes with the same name and I'd like to process only the nodes from a certain path. Any idea? Antje

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 ?

Hi, I have some XML files that have a processing instruction directly after the XML declaration when I do kgroup.reading <- character(0) for (file in file_list){kgroup.reading <- xmlParseDoc(file.path("c:","projects","respositories","dk","004",file))} I get the error file name :1: parser error : Start tag expected, '<' not found