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 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 > > 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 > > 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 >>> >>> 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]]