Hi Anupam, You can find instructions on how to update to the latest versions of R and Bioconductor here: http://www.bioconductor.org/docs/install/ Marc anupam sinha wrote: > 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 at="" 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 at="" 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 at="" 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 at="" 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_COLLAT E=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 at 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 at 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/ >> >> > > > >