[BioC] KEGGsoap: Space required after the Public Identifier

[seth redmond]

I keep running into the same error when trying to do a genes-to-pathways request in the KEGGsoap package: 

I'm new to the package, but as I understand it I should be able to pass a vector of gene IDs and receive back a vector of pathway IDs, however I keep getting a 'xmlns: URI SOAP/KEGG is not absolute' error. This appears to be something to do with the URL for the SOAP server:

>> genes
> [1] "hsa:728819"    "hsa:100129239" "hsa:441150"    "hsa:440905"    "hsa:389493"    "hsa:645954"   
> [7] "hsa:283711"    "hsa:400645"    "hsa:100128416" "hsa:100128542"
>> get.pathways.by.genes(genes)
> xmlns: URI SOAP/KEGG is not absolute
> xmlns: URI SOAP/KEGG is not absolute
> character(0)
>> 
>> KEGGserver <- SOAPServer("http://soap.genome.jp/keggapi/request_v6.0.cgi")
>> .SOAP(KEGGserver, "get_pathways_by_genes",
> +                   .soapArgs=list('genes_id_list' = genes),
> +                   action = KEGGaction, nameSpaces = SOAPNameSpaces(version=1))
> xmlns: URI SOAP/KEGG is not absolute
> xmlns: URI SOAP/KEGG is not absolute
> character(0)
>> 
>> 

There does seem to have been a similar error in relation to the biomaRt package, but I can't see an obvious fix to apply here and I don't seem to be able to find where within the SOAP method this is coming from; if anyone's encountered this before and/or has any advice to offer I'd much appreciate it.

thanks

-s