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. -- Universitätsmedizin Göttingen Abteilung Allgemein- und Viszeralchirurgie Rudolf-Koch-Str. 40 39099 Göttingen -- Dept. of General Surgery University of Göttingen Göttingen, Germany -- http://www.chirurgie-goettingen.de _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
