Hi Ludwig,
I believe you have an older KEGGgraph version. I have 1.2.2 and no problem
to get the xml file. Nevertheless, you can download any xml.
download.file(url="
ftp://ftp.genome.jp/pub/kegg/xml/kgml/metabolic/organisms/cel/cel00010.xml
",destfile="/home/cel00010.xml")
graphpath <- parseKGML2Graph(file="/home/cel00010.xml")
Hope it works
Kachelo

2010/3/29 Ludwig Geistlinger <Ludwig.Geistlinger@campus.lmu.de>

> Dear BioC developers,
>
> as I try to use the retrieveKGML function of the KEGGgraph package, I end
> up with the following error:
>
> ------
>
> retrieveKGML(pathwayid='00010', organism='cel',
> destfile="/home/cbio/ludwig/test.txt", method="wget")
> --17:06:46--  ftp://ftp.genome.jp/pub/kegg/xml/organisms/cel/cel00010.xml
>           => `/home/cbio/ludwig/test.txt'
> Resolving ftp.genome.jp... 133.103.100.184
> Connecting to ftp.genome.jp|133.103.100.184|:21... connected.
> Logging in as anonymous ... Logged in!
> ==> SYST ... done.    ==> PWD ... done.
> ==> TYPE I ... done.  ==> CWD /pub/kegg/xml/organisms/cel ...
> No such directory `pub/kegg/xml/organisms/cel'.
>
> Warning message:
> In download.file(kgml, destfile = destfile, method = method, ...) :
>  download had nonzero exit status
>
> ------
>
> This might be due to a wrong hard coded kegg ftp path inside of KEGGgraph,
> as the recent integration of biopax files has changed the structure of the
> ftp://ftp.genome.jp/pub/kegg/xml/ directory.
> This has destroyed the nice functionality of retrieveKGML.
>
> Kind Regards
>
> Ludwig Geistlinger
> Institute of Infectious Diseases
> University of Cape Town
>
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