Hi David,
               Thanks for your effort. From your session info I come to know
that you are using KEGGgraph_1.3.2 while even after updating the BioC
packages my KEGGgraph version is 1.1.0. Though my XML version is the latest
one .One more thing is that I have an older version(2.4) of BioC. I have a
couple of queries
Can you tell me how to upgrade to the latest version of BioC and R (all my
previous efforts have failed) ?

Can you please send me the the tar ball release of the latest KEGGgraph ?


Thanks and regards,

Anupam Sinha

On Tue, Jan 12, 2010 at 1:32 AM, Jitao David Zhang <davidvonpku@gmail.com>wrote:

> Hi dear Anupam,
>
>   I have tried the script, but I cannot replicate your error. Therefore it
> would be helpful if you could check the version of R and KEGGgraph you use.
> Following is my session info
>
> >sessionInfo()
> R version 2.11.0 Under development (unstable) (2009-11-07 r50345)
> i686-pc-linux-gnu
>
> locale:
>  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=de_DE.UTF-8
>  [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices datasets  utils     methods
> [8] base
>
> other attached packages:
> [1] KEGGgraph_1.3.2  Rgraphviz_1.23.2 graph_1.25.3     XML_2.6-0
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.0
>
>   The XML files could be parsed without any error.
>
>   Best wishes,
> David
>
> 2010/1/11 anupam sinha <anupam.contact@gmail.com>
>
> Hi David and Wolfgang,
>>                                     Thanks a lot for our suggestions. I
>> updated the packages (both R and Bioconductor). But still the same error
>> message.Apologies for not stating my problem clearly and this time I will
>> provide the files . I will have another go at it. I have this folder by name
>> ORG_XML_FILES  where I need to run my R script. This folder contains
>> directories for organisms which in turn contain the pathways in KGML format.
>> So I start from ORG_XML_FILES directory and decend into each of the
>> individual subdirectory (having KGML files of a specific organism). Read all
>> these KGML files to a list and construct a metabolic network. Next step is
>> to come out of this subdirectory into ORG_XML_FILES and then descend into
>> next subdirectory repeat the operation. I have written a script for it and
>> it doesn't seem to be working. Gives error:
>>
>>
>> Error in UseMethod("xmlAttrs", node) :
>>  no applicable method for "xmlAttrs"
>>
>> I am forwarding three files. Two of the files are the zipped folders of
>> pathways of organisms (KGML format).
>> Third is my script.
>>
>> *aac is the KEGG organism identifier for Alicyclobacillus acidocaldarius
>> aae is the KEGG organism identifier for Aquifex aeolicus
>> *
>> Apologies if the mail is bit long.
>>
>> Regards,
>>
>> Anupam
>>
>>
>>
>> On Mon, Jan 11, 2010 at 2:33 AM, Jitao David Zhang <davidvonpku@gmail.com
>> > wrote:
>>
>>> @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]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor@stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>
>>>> --
>>>>
>>>> Best wishes
>>>>     Wolfgang
>>>>
>>>>
>>>> --
>>>> Wolfgang Huber
>>>> EMBL
>>>> http://www.embl.de/research/units/genome_biology/huber/contact
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor@stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> 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/
>>>
>>
>>
>>
>> --
>> Graduate Student,
>> Laboratory of Computtational Biology,
>> Centre For DNA Fingerprinting And Diagnostics,
>> 4-1-714 to 725/2, Tuljaguda complex
>> Mozamzahi Road, Nampally,
>> Hyderabad-500001
>>
>
>
>
> --
> Jitao David Zhang
> Biological Statistics and Computational Biology Ph.D.
> Division of Molecular Genome Analysis
> DKFZ, Heidelberg D-69120, Germany
>
> http://www.NextBioMotif.com/
>



-- 
Graduate Student,
Laboratory of Computtational Biology,
Centre For DNA Fingerprinting And Diagnostics,
4-1-714 to 725/2, Tuljaguda complex
Mozamzahi Road, Nampally,
Hyderabad-500001

	[[alternative HTML version deleted]]

