Hi Markus and to all bioconductor users,

  Thank you for the feedback. I have contacted staffs at KEGG and confirmed
that the error is caused by an inconsistent update of KGML files - their
current version of XML files are missing 'reaction' items and not complete.

  Therefore we have to wait the KEGG to update their files again. I will
post here by then.

  Thank you very much again for the report and sorry for the inconvenience.

  Best wishes,
Jitao David Zhang

2009/4/17 Markus Schmidberger <schmidb@ibe.med.uni-muenchen.de>

> Hi,
>
> I found the KEGGgraph package in the development repository. It sounds
> great. But it is not working. There are no edges in the graphs!
> What is wrong?
>
> > library(KEGGgraph)
> > tmp <- tempfile()
> > retrieveKGML('04110', organism="hsa", destfile=tmp, method="wget",
> quiet=FALSE)
> --08:58:59--  ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04110.xml
>          => `/tmp/3127.1.maxmem.q/Rtmpe1YxAS/file643c9869'
> Auflösen des Hostnamen »ftp.genome.jp«.... 133.103.100.184
> Verbindungsaufbau zu ftp.genome.jp|133.103.100.184|:21... verbunden.
> Anmelden als anonymous ... Angemeldet!
> ==> SYST ... fertig.    ==> PWD ... fertig.
> ==> TYPE I ... fertig.  ==> CWD /pub/kegg/xml/organisms/hsa ... fertig.
> ==> PASV ... fertig.    ==> RETR hsa04110.xml ... fertig.
> Länge: 27.902 (27K) (unmaßgeblich)
>
> 100%[==============================================================>]
> 27.902        29.55K/s
> 08:59:04 (29.51 KB/s) - »/tmp/3127.1.maxmem.q/Rtmpe1YxAS/file643c9869«
> gespeichert [27902]
>
> > file.rename(tmp, paste(tmp,".xml",sep=""))
> [1] TRUE
> > tmp <- paste(tmp,".xml",sep="")
> > kegg <- parseKGML2Graph(tmp, expandGenes=T, genesOnly=T )
> Fehler in subGraphByNodeType(gR, "gene") :
>  No 'gene' type found in the file, maybe it is a map file. Please try
> parsing the file with 'genesOnly=FALSE'
>
>
> > parseKGML(tmp)
> KEGG Pathway
> [ Title ]: Cell cycle
> [ Name ]: path:hsa04110
> [ Organism ]: hsa
> [ Number ] :04110
> [ Image ] :http://www.genome.jp/kegg/pathway/hsa/hsa04110.gif
> [ Link ] :http://www.genome.jp/dbget-bin/show_pathway?hsa04110
> ------------------------------------------------------------
> Statistics:
>       99 node(s)
>       0 edge(s)
>       0 reaction(s)
> ------------------------------------------------------------
> >
>
> > sessionInfo()
> R version 2.8.0 (2008-10-20)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=de_DE@euro
> ;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE.UTF-8;LC_MONETARY=C;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   grid      tools     stats     graphics  grDevices utils   [8]
> datasets  methods   base
> other attached packages:
> [1] org.Hs.eg.db_2.2.6  KEGGgraph_0.8.16    XML_1.98-1        [4]
> hgu133acdf_2.3.0    vsn_3.8.0           limma_2.16.2      [7]
> lattice_0.17-15     GeneNet_1.2.3       fdrtool_1.2.5     [10]
> longitudinal_1.1.4  corpcor_1.5.2       genefilter_1.22.0 [13]
> survival_2.34-1     hgu133a.db_2.2.5    RSQLite_0.7-1     [16] DBI_0.2-4
>       AnnotationDbi_1.4.0 pcalg_0.1-7       [19] mnormt_1.3-2
>  ggm_1.0.2           Rgraphviz_1.20.0  [22] robustbase_0.4-5    graph_1.19.6
>        MASS_7.2-44       [25] affy_1.20.0         Biobase_2.2.0
> loaded via a namespace (and not attached):
> [1] affyio_1.10.1        annotate_1.20.0      cluster_1.11.11    [4]
> preprocessCore_1.4.0
>
>
>
>
> Thanks
> Markus
>
>
>
> --
> Dipl.-Tech. Math. Markus Schmidberger
>
> Ludwig-Maximilians-Universität München
> IBE - Institut für medizinische Informationsverarbeitung,
> Biometrie und Epidemiologie
> Marchioninistr. 15, D-81377 Muenchen
> URL: http://www.ibe.med.uni-muenchen.de Mail: Markus.Schmidberger [at]
> ibe.med.uni-muenchen.de
> Tel: +49 (089) 7095 - 4497
>
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>



-- 
Cheers,
David

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