[BioC] problem with get.genes.by.pathway
Kimpel, Mark William
mkimpel at iupui.edu
Tue Oct 4 00:22:23 CEST 2005
I have been working through examples in the new book
"Bioinformatics and Computational Biology Solutions Using R and Bioconductor" ISBN:0387251464
The following code chunk leads to an error message. Any ideas on what the problem could be? SessionInfo follows.
library("KEGG")
library("KEGGSOAP")
genes <- get.genes.by.pathway("path:eco00020")
Error in curlPerform(url = url, httpheader = header, postfields = txt, :
Failed writing header
1: get.genes.by.pathway("path:eco00020")
2: unlist(.SOAP(KEGGserver, "get_genes_by_pathway", .soapArgs = list(pathway_id = pathway.id), action = KEGGaction, xmlns = KEGGxmlns))
3: .SOAP(KEGGserver, "get_genes_by_pathway", .soapArgs = list(pathway_id = pathway.id), action = KEGGaction, xmlns = KEGGxmlns)
4: curlPerform(url = url, httpheader = header, postfields = txt, writeFunction = bodyDataFun$update, headerFunction = headerDataFun$update, .opts = .opts)
R version 2.2.0, 2005-08-29, i386-pc-mingw32
attached base packages:
[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base"
other attached packages:
KEGGSOAP SSOAP RCurl XML KEGG limma affy reposTools Biobase RWinEdt
"1.1.1" "0.2-1" "0.5-1" "0.97-8" "1.8.1" "2.0.8" "1.7.2" "1.6.2" "1.7.0" "1.7-3"
Mark W. Kimpel MD
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Department of Psychiatry
Indiana University School of Medicine
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