Hi Fraser,

Works for me:

> 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)
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)
------------------------------------------------------------

This might have something to do with your internet connection, since it does
not seem to be either the package nor the repository (but I am using a
different version of R so this is not exactly a reproduction of your code).

> sessionInfo()
R version 2.11.0 Under development (unstable) (2009-10-04 r49936)
i386-apple-darwin10.0.0

locale:
[1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8

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

other attached packages:
[1] KEGGgraph_1.1.12 Rgraphviz_1.23.5 graph_1.23.7     XML_2.6-0

loaded via a namespace (and not attached):
[1] tools_2.11.0

Cheers,
--Tony

On Tue, Oct 13, 2009 at 7:59 AM, Fraser Sim <fjsim@buffalo.edu> wrote:

> 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
> IE/Firefox.
>
> 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
> "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml"
> Error: 1: failed to load external entity
> "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml"
> > sessionInfo()
> R version 2.9.1 (2009-06-26)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=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
> >
>
> Thanks,
> Fraser
>
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