[BioC] KEGGgraph problem

[Zhang, Jitao David]

Hello,

  If you check the value of "cancerKGML" , it turns out to be an empty string. Actually the file does not exist.

  For an working example, use system.file("extdata/hsa05210.xml", package="KEGGgraph"). Or use your own KGML file.

   Best wishes,
David
-----Original Message-----
From: eric [guest] [mailto:guest at bioconductor.org] 
Sent: Dienstag, 29. Januar 2013 17:49
To: bioconductor at r-project.org; aetc23_98 at yahoo.com
Cc: Zhang, Jitao David {PNBE~Basel}
Subject: KEGGgraph problem



Hi All,

I am running into a problem with KEGGgraph package. After loading all libraries and downloading hsa05200.xml I run:

cancerKGML <- system.file("hsa05200.xml",package="KEGGgraph");

but then, on running

cancerG <- parseKGML2Graph(cancerKGML,expandGenes=TRUE);

I get:
Error: XML content does not seem to be XML, nor to identify a file name ''

Any ideas? Many thanks,
Eric





 -- output of sessionInfo(): 

R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] org.Hs.eg.db_2.7.1   KEGG.db_2.7.1        RSQLite_0.11.2      
 [4] DBI_0.2-5            AnnotationDbi_1.18.4 Biobase_2.16.0      
 [7] BiocGenerics_0.2.0   KEGGgraph_1.12.0     graph_1.34.0        
[10] XML_3.95-0.1        

loaded via a namespace (and not attached):
[1] IRanges_1.14.4 stats4_2.15.0  tools_2.15.0  

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