[BioC] Problem with KEGGgraph

Fraser Sim fjsim at buffalo.edu
Tue Oct 13 16:59:10 CEST 2009

Dear all,

I'm having a problem with KEGGgraph. It appears the problem is located on
the KEGG servers as I am unable to download the xml directly using

Here's the code:

> library(KEGGgraph)
> url <- getKGMLurl('04330', organism = "hsa")
> url
[1] ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml
> parseKGML(url)
failed to load external entity
Error: 1: failed to load external entity
> sessionInfo()
R version 2.9.1 (2009-06-26) 

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
 [1] hgu133plus2.db_2.2.11 org.Hs.eg.db_2.2.11   Rgraphviz_1.21.11    
 [4] KEGGgraph_1.0.0       graph_1.22.2          XML_2.3-0            
 [7] KEGG.db_2.2.11        RSQLite_0.7-1         DBI_0.2-4            
[10] AnnotationDbi_1.6.1   Biobase_2.4.1         rcom_2.2-1           
[13] rscproxy_1.3-1       

loaded via a namespace (and not attached):
[1] annotate_1.22.0   genefilter_1.24.2 splines_2.9.1     survival_2.35-4  
[5] tools_2.9.1       xtable_1.5-5     


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