[BioC] Error in keggPathwayGraphs when updateCache = TRUE

[Shruti Marwaha [guest]]

Dear List & Calin,

I am trying to use Pathway Express from RontoTools for microarray analysis. I get the following error with keggPathwayGraphs command when I use the option "updateCache = TRUE". I want to use this option in order to download the latest KEGG pathways.

Thanks & Regards,
Shruti Marwaha

Graduate Student
Systems Biology and Physiology
University of Cincinnati

 -- output of sessionInfo(): 

> library("KEGGREST")
> library("ROntoTools")
> kpg <- keggPathwayGraphs("hsa", updateCache = TRUE, verbose = F)
NA element in edges.
Error in validObject(.Object) : invalid class “graphNEL” object: FALSE

> traceback()
15: stop(msg, ": ", errors, domain = NA)
14: validObject(.Object)
13: .local(.Object, ...)
12: initialize(value, ...)
11: initialize(value, ...)
10: new("graphNEL", nodes = nodes, edgeL = edgeL, edgemode = edgemode)
9: graphNEL(nodes = snodes, edgeL = newEdges, edgemode = edgemode(graph))
8: subGraph(nodes, graph)
7: subGraph(nodes, graph)
6: subKEGGgraph(new.nodes, graph)
5: subGraphByNodeType(gR, "gene")
4: KEGGgraph::KEGGpathway2Graph(g)
3: FUN(X[[82L]], ...)
2: lapply(allPathwayInfo, function(g) {
       g <- KEGGgraph::KEGGpathway2Graph(g)
       kg <- new("graphNEL", nodes(g), edges(g), edgemode = "directed")
       if (length(getKEGGedgeData(g)) == 0) {
           if (verbose) 
               setTxtProgressBar(pb, getTxtProgressBar(pb) + 1)
           return(NULL)
       }
       edgeDataDefaults(kg, "subtype") <- NA
       relGeneTable <- data.frame(cbind(do.call(rbind, strsplit(names(getKEGGedgeData(g)), 
           "~")), sapply(getKEGGedgeData(g), function(e) paste(lapply(getSubtype(e), 
           getName), collapse = ","))), stringsAsFactors = FALSE)
       names(relGeneTable) <- c("from", "to", "subtype")
       edgeData(kg, relGeneTable$from, relGeneTable$to, "subtype") <- relGeneTable$subtype
       if (verbose) 
           setTxtProgressBar(pb, getTxtProgressBar(pb) + 1)
       return(kg)
   })
1: keggPathwayGraphs("hsa", updateCache = TRUE, verbose = F)


> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ROntoTools_1.4.0 Rgraphviz_2.8.1  KEGGgraph_1.22.1 XML_3.98-1.1     boot_1.3-11      graph_1.42.0    
[7] KEGGREST_1.4.1  

loaded via a namespace (and not attached):
 [1] BiocGenerics_0.10.0 Biostrings_2.32.1   httr_0.4            IRanges_1.22.10     parallel_3.1.0     
 [6] png_0.1-7           RCurl_1.95-4.3      stats4_3.1.0        stringr_0.6.2       tools_3.1.0        
[11] XVector_0.4.0       zlibbioc_1.10.0


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