[BioC] KEGGgraph bug

[Fraser Sim]

I have found a problem with how 'getKGMLurl' constructs the URL for
retrieving the KGML files. It looks like the '_' should be '-' in
non_metabolic portion of the generated url. I am using the current release
versions, R2.10.0 and KEGGgraph 1.2.0.

Thanks,
Fraser

> library(KEGGgraph)
Loading required package: XML
Loading required package: graph

Attaching package: 'graph'


        The following object(s) are masked from package:XML :

         addNode 

Loading required package: Rgraphviz
Loading required package: grid
> url <- getKGMLurl('04330', organism = "hsa")
> url
[1]
"ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa04330.
xml"
> parseKGML(url)
failed to load external entity
"ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa04330.
xml"
Error: 1: failed to load external entity
"ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa04330.
xml"
> parseKGML(gsub("_","-",url))
KEGG Pathway
[ Title ]: Notch signaling pathway
[ Name ]: path:hsa04330
[ Organism ]: hsa
[ Number ] :04330
[ Image ] :http://www.genome.jp/kegg/pathway/hsa/hsa04330.png
[ Link ] :http://www.genome.jp/kegg-bin/show_pathway?hsa04330
------------------------------------------------------------
Statistics:
        30 node(s)
        16 edge(s)
        0 reaction(s)
------------------------------------------------------------
> sessionInfo()
R version 2.10.0 (2009-10-26) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United
States.1252    

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

other attached packages:
[1] KEGGgraph_1.2.0  Rgraphviz_1.24.0 graph_1.24.0     XML_2.6-0
rcom_2.2-1       rscproxy_1.3-1  

loaded via a namespace (and not attached):
[1] tools_2.10.0
>