[R] Analyzing Publications from Pubmed via XML

David Winsemius dwinsemius at comcast.net
Tue Dec 18 21:39:36 CET 2007

"Armin Goralczyk" <agoralczyk at gmail.com> wrote in
news:a695fbee0712180702k1a351b5cxca54d45b81096166 at mail.gmail.com: 

> On 12/18/07, David Winsemius <dwinsemius at comcast.net> wrote:
>> David Winsemius <dwinsemius at comcast.net> wrote in
>> news:Xns9A09CA51DB1E4dNOTwinscomcast at
>> > "Armin Goralczyk" <agoralczyk at gmail.com> wrote in
>> > news:a695fbee0712171238g4995040x579e58f52f83376e at mail.gmail.com:
>> >> I tried the above function with simple search terms and it worked
>> >> fine for me (also more output thanks to Martin's post) but when I
>> >> use search terms attributed to certain fields, i.e. with [au] or
>> >> [ta], I get the following error message:
>> >>> pm.srch()
>> >> 1: "laryngeal neoplasms[mh]"
>> >> 2:
>> > I am wondering if you used spaces, rather than "+"'s? If so then
>> > you may want your function to do more gsub-processing of the input
>> > string. 
>> I tried my theory that one would need "+"'s instead of spaces, but
>> disproved it. Spaces in the input string seems to produce acceptable
>> results on my WinXP/R.2.6.1/RGui system even with more complex search
>> strings.
>> --
> 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. 

David Winsemius

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