On Dec 18, 2007 9:39 PM, David Winsemius <[EMAIL PROTECTED]> wrote: > "Armin Goralczyk" <[EMAIL PROTECTED]> wrote in > news:[EMAIL PROTECTED]: > > > It's not the spaces, the problem is the tag (sorry that I didn't > > specify this), or maybe the string []. I am working on a Mac OS X 10.4 > > with R version 2.6. Is it maybe a string conversion problem? In the > > following warning strings in the html adress seem to be different: > > 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&ter > > m=laryngeal neoplasms[mh] > > I/O warning : failed to load external entity > > "http%3A//eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi%3Fdb=pubme > > d&term=laryngeal%20neoplasms%5Bmh%5D" > > I do not have an up-to-date version of R on my Mac, since I have not yet > upgraded to OSX10.4. I can try with my older version of R, but failure > (or even success) with versions OSX-10.2/R-2.0 is not likely to be very > informative. If you will post an example of the input that is resulting > in the error, I can try it on my WinXP machine. If we cannot reproduce it > there, then it may be more appropriate to take further questions to the > Mac-R mailing list. The error message suggests to me that the fault lies > in the connection phase of the task. >
Example: > 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) #search successfull > > 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" > Seems to be a Mac problem. I will post on the Mac-R mailing list. Thanks -- Armin ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.