[BioC] KEGGgraph, error

[Markus Schmidberger]

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 at 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