[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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