[R] Directory operations

[Seth Falcon]

On 1/10/10 5:46 AM, anupam sinha wrote:
> Hi Uwe,
>               Thanks for your suggestion . Here's my code. I am confused as
> to how to initialize an empty list . Here I have used pairlist()
>
>
>   *list.files()->org_xml_dirs

## the following is much preferred:

org_xml_dirs <- list.files()

>   for (i in org_xml_dirs)
> {
>   setwd(file.path("/home/anupam/Research/Anupam_data/ORG_XML_FILES/",i))
>   org_xml<-list.files()
>   for(j in org_xml)
>   {
>   graph_list<-pairlist()

graph_list <- list() ## in general, avoid pairlist

>   graph<-parseKGML2Graph(j,genesOnly=TRUE)
>   graph_list<-c(graph_list,list(graph))
>   }
>   org_met_net<-mergeKEGGgraphs(graph_list)
>   met_org<-igraph.from.graphNEL(org_met_net,name=TRUE)
>   write.graph(met_org,"/home/anupam/Research/Anupam_data/ORG_XML_FILES/i.metnet",format=c("NCOL"))
>   }
> *
> This is giving an error:
>
> Error in UseMethod("xmlAttrs", node) :
>    no applicable method for "xmlAttrs"
>
> I apologise for asking a Bioconductor list related question on this list.
> Can you figure out the problem ? Thanks in advance.

Without output of sessionInfo() it is hard to diagnose further, but this 
looks like a bug that has been resolved in latest version of the XML 
package.  Please make sure you are using the latest R release and latest 
Bioconductor and CRAN packages.

+ seth

-- 
Seth Falcon
Bioconductor Core Team | FHCRC