[BioC] KEGGSOAP

[Dr.Mayhaus Manuel]

Thanks Nianhua,

I had been trying the devel-version as well ... with no results.
Now having changed the URL it works !

best

Manuel Mayhaus
Genopolis Consortium
(+39) 02 6448 3530
http://www.genopolis.it


On Mar 20, 2006, at 8:42 PM, Nianhua Li wrote:

> 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
>
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