[BioC] KEGGSOAP

[Nianhua Li]

Dear Dr. Mayhaus Manuel,

The problem is due to an update at KEGG server. They modified the port 
url from "http://soap.genome.ad.jp/keggapi/request.cgi" into 
"http://soap.genome.ad.jp/keggapi/request_v5.0.cgi". You could check out 
an updated version of KEGGSOAP from devel repository or you could update 
the KEGGserver object:

 > library(KEGGSOAP)
Loading required package: XML
Loading required package: SSOAP
Loading required package: RCurl
Loading required package: RCurl
 > get.pathways.by.genes(c("eco:b0077", "eco:b0078"))
Error in .SOAP(KEGGserver, "get_pathways_by_genes", .soapArgs = 
list(genes_id_list= genes.id.list),  :
       Error occurred in the HTTP request: Failed to access class 
(SOAP::KEGG): Can't locate File/Basename.pm in @INC (@INC contains: 
/usr/local/WWW/pub/kegg/soap/cgi-bin 
/usr/local/WWW/cgi/kegg/ligand-bin/PACKAGE 
/usr/local/WWW/cgi/kegg/ligand-bin/DBIF 
/usr/local/WWW/cgi/kegg/ssdb-bin/package/GFIT_DBIF 
/usr/local/WWW/cgi/kegg/ssdb-bin/package/SS_DBIF 
/usr/local/WWW/pub/kegg/soap) at 
/usr/local/WWW/pub/kegg/soap/SOAP/KEGG.pm line 14.
BEGIN failed--compilation aborted at 
/usr/local/WWW/pub/kegg/soap/SOAP/KEGG.pm line 14.
Compilation failed in require at (eval 89) line 3.
 >
 > KEGGserver
An object of class "HTTPSOAPServer"
Slot "host":
[1] "soap.genome.ad.jp"

Slot "port":
[1] NA

Slot "url":
[1] "/keggapi/request.cgi"

 > KEGGserver at url <- "/keggapi/request_v5.0.cgi"

 > get.pathways.by.genes(c("eco:b0077", "eco:b0078"))
[1] "path:eco00290" "path:eco00650" "path:eco00660" "path:eco00770"
 > mark.pathway.by.objects ("path:eco00260", c("eco:b0002", "eco:c00263"))
[1] "http://soap.genome.jp/tmp/mark_pathway_www2_api29687/eco00260.gif"

thanks

nianhua
Program in Computational Biology
Fred Hutchinson Cancer Research Center