[BioC] KEGGgraph, error

Jitao Zhang j.zhang at dkfz-heidelberg.de
Fri Apr 17 10:11:30 CEST 2009


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By the way, in the extdata directory of KEGGgraph package, there are
several valid KGML files for the demo of KEGGgraph package
functionality. Before the issue is fixed by KEGG database, one could
also use these files (data stand November 2008)

kgmlFile <- system.file("extdata/hsa04110.xml", package="KEGGgraph")
graph <- parseKGML2Graph(kgmlFile)

Best wishes,
David

Jitao Zhang wrote:

> Hi dear Markus,
> 
>   Thanks for your feedback. It seems that the error is caused by an
> mistake in the update of KEGG database - their current version of XMLs
> are not complete. Therefore for now I do not think it is a bug of KEGGgraph.
> 
>   I will write to the maintainer of KEGG database to suggest the problem
> of the XMLs and will udpate you when it is okay again.
> 
>   Best wishes,
> David
> 
> Markus Schmidberger wrote:
>> 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
> 
> 
> 
> 
> 

- --
THINK BEFORE YOU PRINT: DO OUR ENVIRONMENT GOOD

Jitao David Zhang
Computational Biology/Bioinformatics Ph.D. Candidate
Division of Molecular Genome Analysis, DKFZ
Im Neuenheimer Feld 580,
Heidelberg D-69120
Germany

Tel: 49-(0)6221-424711
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