Hi dear Yan,

  You could manually download the file from KEGG server, in case wget does
not work out of any reason. Note that system.file function only provides the
possibility to access the file delivered together with the package, but not
the ones that you download after the installation of KEGGgraph. To do that,

  (1) download the file to a location (for example, C:/KEGGgraph/ in
windows, or /home/username/KEGGgraph in linux)
  (2) in R, assign the actual file location, for example

   colFile <- "C:/KEGGgraph/has05211.xml"

  (3) call paseKGML2Graph(colFile)

  Best wishes,
David

2010/11/29 Yan Jiao <y.jiao@ucl.ac.uk>

> Hi
>
>
>
> I'm trying to ues retrieveKGML from KEGGgraph package:
>
>  retrieveKGML(pathwayid="05211", organism="hsa", destfile=tmp)
>
> Warning message:
>
> In download.file(kgml, destfile = destfile, method = method, ...) :
>
>  download had nonzero exit status
>
>  colFile <- system.file("extdata/hsa05211.xml",package="KEGGgraph")
>
>  g <- parseKGML2Graph(colFile)
>
> Error:   does not seem to be XML, nor to identify a file name
>
>
>
> as you can see I got warning message, is it ok? I don't think it worked
> properly, since I got error after I ran parse KGML2Graph,
>
> I guess i need to install wget, but can't find wget for win 64.
>
>
>
>
>
> any suggestion?
>
>
>
> many thanks
>
>
>
> yan
>
>
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-- 
Jitao David Zhang
Pre-doc staff of Computational Biology and Biostatistics
Division of Molecular Genome Analysis
DKFZ, Heidelberg D-69120, Germany

http://www.NextBioMotif.com/

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