Message-ID: <a695fbee0712190201u15dfec8dqa63cd44818130ddc@mail.gmail.com>
Date: 2007-12-19T10:01:56Z
From: Armin Goralczyk
Subject: Failure message in R on Mac with xmlTreeParse
Hello
In the following thread (R-help) the possibilities of analyzing
publications from pubmed via XML were discussed:
http://www.nabble.com/Analyzing-Publications-from-Pubmed-via-XML-to14328779.html#a14343090
Using xmlTreeParse in a function results in a failure message on my
Mac which is not reproduced in R for Windows:
> esearch <- function (term){
+ srch.stem <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
+ srch.mode <- "db=pubmed&retmax=10000&retmode=xml&term="
+ doc <-xmlTreeParse(paste(srch.stem,srch.mode,term,sep=""),isURL = TRUE,
+ useInternalNodes = TRUE)
+ sapply(c("//Id"), xpathApply, doc = doc, fun = xmlValue)
+ }
>
> term <- 'meyer'
> pmid <- esearch(term) # works fine
>
> term <- 'meyer[au]'
> pmid <- esearch(term)
Fehler in .Call("RS_XML_ParseTree", as.character(file), handlers,
as.logical(ignoreBlanks), :
error in creating parser for
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=10000&retmode=xml&term=meyer[au]
>
I/O warning : failed to load external entity
"http%3A//eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi%3Fdb=pubmed&retmax=10000&retmode=xml&term=meyer%5Bau%5D"
>
The problem seems to be the search tag [au].
I am not very familiar with XML or the xmlTreeParse function, so I
don't know what is wrong. Can anybody help?
Thanks
My version:
> R.Version()
$platform
[1] "powerpc-apple-darwin8.10.1"
$arch
[1] "powerpc"
$os
[1] "darwin8.10.1"
$system
[1] "powerpc, darwin8.10.1"
$status
[1] "Patched"
$major
[1] "2"
$minor
[1] "6.0"
$year
[1] "2007"
$month
[1] "11"
$day
[1] "09"
$`svn rev`
[1] "43408"
$language
[1] "R"
$version.string
[1] "R version 2.6.0 Patched (2007-11-09 r43408)"
--
Armin Goralczyk, M.D.
--
Universit?tsmedizin G?ttingen
Abteilung Allgemein- und Viszeralchirurgie
Rudolf-Koch-Str. 40
39099 G?ttingen
--
Dept. of General Surgery
University of G?ttingen
G?ttingen, Germany
--
http://www.chirurgie-goettingen.de