[R] Error Using pm.getabst()

lars larsenmtl at comcast.net
Fri Aug 13 04:20:47 CEST 2004


Thank you for your reply.  I thought RSXML was an R (CRAN) package? I
realize your package is part of bioconductor so I'll try the
bioconductor mailing list as well.  

Also and more importantly I took your suggestion and stepped through the
calls.   It seems the failure in pm.getabst() occurs when creating absts
with the pubmed function.  When I'm back at work, I'll have to research
why it fails further.  Right now, while I'm at home, it works

Any reason this would fail behind a corporate firewall as opposed to my
home network?

Oh and my apologies for posting so hastily without the full
information.  R - 1.9.1, annotate - 1.4.0, RSXML - 0.97, all on a
Windows2000 OS.


Mark Larsen

On Thu, 2004-08-12 at 17:28, Robert Gentleman wrote: 
> You will almost surely do better to ask about Bioconductor packages on
> the Bioconductor mailing list. Next, it is helpful to know what
> versions of things you are using.
> As for your problem, did you look to see what kind of object absts is?
> There seems to be no default method for xmlRoot, and it is likely that
> the call to create the absts object failed (prior to this). You might
> want to try stepping through the commands, one at a time and checking
> each step. Often, the problem arises because you have not properly set
> up your connection to the internet and so none of the querying
> software will work.
>   Robert
> On Thu, Aug 12, 2004 at 08:20:10PM +0000, larsenmtl at comcast.net wrote:
> > R Users:
> > 
> > After installing Bioconductor, RSXML and all the relevant Win32 DLLs (libxml2, zlib, iconv), I receive the following error message when using pm.getabst()
> > 
> > Error in xmlRoot(absts) : no applicable method for "xmlRoot"
> > 
> > I receive this when using the example from help(pm.getabst).  
> > 
> > Downloading the target XML file, parsing it with xmlTreeParse and applying xmlRoot returns no error.
> > 
> > Your thoughts/suggestions are appreciated.
> > 
> > Mark Larsen
> > 
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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