[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
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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