[BioC] KEGGgraph: retrieveKGML error (due to wrong ftp path)

Ludwig Geistlinger Ludwig.Geistlinger at campus.lmu.de
Mon Mar 29 17:15:59 CEST 2010

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...
Connecting to ftp.genome.jp||: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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