@Wolfgang: Thank you very much for the good tip!

Hi dear Anupam,

  Exactly, Wolfgang made the point. It is a known issue related to the old
XML package, and has been long solved since the version 1.1.x. Please
therefore update R, Bioconductor and KEGGgraph.

  Best wishes,
David


2010/1/10 Wolfgang Huber <whuber@embl.de>

> Dear Anupam
>
> the first thing you should try is upgrading to the most recent version of R
> and Bioconductor.
>
> Next, if that does not help, please provide a reproducible example (others
> cannot see the files in your /home/anupam/ directory and hence not reproduce
> your problem, which almost always is a prerequisite for providing help).
>
>        Best wishes
>        Wolfgang
>
>
>  Hi all,
>>         I have downloaded the KGML files of for all the pathways of some
>> organisms . I want to automate the process of constructing the metabolic
>> networks of these organisms. In a directory by name ORG_XML_FILES I have
>> the
>> following directories and  files
>>
>> /aac(dir)       /aae(dir)          etc ......
>> 1.xml           4.xml
>> 2.xml           5.xml
>> 3.xml           6.xml
>>
>> I want to enter each subdirectory (for e.g. aac) read all the xml files
>> and
>> construct a metabolic network using KEGGgraph
>>
>> I have written the following script:
>>
>> setwd("/home/anupam/Research/Anupam_data/ORG_XML_FILES/")
>>  list.files()->org_xml_dirs
>>  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<-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"))
>>  }
>>
>> But it is giving the following error :
>>
>> Error in UseMethod("xmlAttrs", node) :
>>  no applicable method for "xmlAttrs"
>>
>>
>> here's my sessioninfo.
>>
>>  sessionInfo()
>>>
>> R version 2.9.0 (2009-04-17)
>> x86_64-redhat-linux-gnu
>>
>> locale:
>>
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] KEGGgraph_1.1.0 graph_1.22.2    XML_2.5-1       igraph_0.5.2-2
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.9.0
>>
>>
>> Can anyone help me out with this ? thanks in advance.
>>
>> Regards,
>>
>> Anupam
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>
> --
>
> Best wishes
>     Wolfgang
>
>
> --
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber/contact
>
>
> _______________________________________________
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> Bioconductor@stat.math.ethz.ch
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> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Jitao David Zhang
Biological Statistics and Computational Biology Ph.D.
Division of Molecular Genome Analysis
DKFZ, Heidelberg D-69120, Germany

http://www.NextBioMotif.com/

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