Hi David, So I've done some testing, and it appears that assuming my list has no NULL elements it works fine. Tested on: [ko00010.xml, ko00020.xml, ko00030.xml,ko00040.xml] The moment there are NULL graphs (in the metabolic/ko folder there are 12) it produces the error. Interestingly, it produces the error even after I've - or assumed I'd removed - the null entries using: AllGraphs[sapply(AllGraphs, is.null)] <- NULL or AllGraphs <- AllGraphs[!sapply(AllGraphs, is.null)] Both of which remove the 12 entries. This used to work fine. As you asked, I've worked out which entries are NULL (these were NULL in 1.16.0 as well). I am unable to do the whole of KEGG at home, so this is just the NULL entries from metabolic/ko: ko00121.xml ko00190.xml ko00195.xml ko00196.xml ko00271.xml ko00312.xml ko00511.xml ko00514.xml All these produce the: 'The pathway contains no chemical reactions!' warning. Hope this helps, Stuart On Thu, Oct 17, 2013 at 2:58 AM, Zhang, Jitao David < jitao_david.zhang@roche.com> wrote: > Dear Stuart, > > The uniqueReaction option has been deleted in the latest release. > > Could you tell which graph was NULL from AllGraphs? And the KGML file > of that? If so I can have a deeper look into the issue. > > Best, > David > > > On Wed, Oct 16, 2013 at 9:50 AM, Stuart Bradley wrote: > >> Right final email before I go to sleep. Probably should've kept these >> together. Apologies! >> >> After removing uniqueReaction = FALSE, the: FinalGraph <- >> mergeKEGGgraphs(AllGraphs, edgemode = "directed") ; line throws the >> following error: >> >> Error in (function (classes, fdef, mtable) : >> unable to find an inherited method for function ‘getName’ for signature >> ‘"NULL"’ >> >> Is that likely to be related? Or something else entirely? >> >> Cheers, >> Stuart >> >> >> On Wed, Oct 16, 2013 at 8:27 PM, Stuart Bradley wrote: >> >>> Ok found the actual culprit. It appears UniqueReaction = FALSE is an >>> unused argument in KEGGpathway2reactionGraph. Did this change? Or is >>> something funny going on? I've used it previously. >>> >>> Stuart >>> >>> >>> On Wed, Oct 16, 2013 at 8:18 PM, Stuart Bradley wrote: >>> >>>> Correction; Error hasn't disappeared; KEGGpathway2reactionGraph is >>>> returning all NULL entries. >>>> >>>> >>>> On Wed, Oct 16, 2013 at 7:53 PM, Stuart Bradley >>> > wrote: >>>> >>>>> Hi David, >>>>> >>>>> Appears to be working as normal on my laptop now. Not sure why, >>>>> haven't changed anything. But the error has dissappeared. Will use exact >>>>> files from laptop on the workstation on Monday to confirm it's a non-issue. >>>>> >>>>> Cheers, >>>>> Stuart >>>>> >>>>> >>>>> On Tue, Oct 15, 2013 at 9:47 PM, Zhang, Jitao David < >>>>> jitao_david.zhang@roche.com> wrote: >>>>> >>>>>> Dear Stuart, do you have an idea which file broke the code? >>>>>> >>>>>> Best, David >>>>>> >>>>>> >>>>>> On Mon, Oct 14, 2013 at 6:48 PM, Stuart Bradley < >>>>>> stuy.bradley@gmail.com> wrote: >>>>>> >>>>>>> Hi all, >>>>>>> >>>>>>> 1.19.0 appears to break our code (tried it on my laptop this >>>>>>> morning) see: https://gist.github.com/lutrasdebtra/6978575 for code >>>>>>> and Session Info. >>>>>>> >>>>>>> Cheers, >>>>>>> Stuart >>>>>>> >>>>>>> >>>>>>> On Mon, Oct 14, 2013 at 7:21 PM, Stuart Bradley < >>>>>>> stuy.bradley@gmail.com> wrote: >>>>>>> >>>>>>>> Hi folks, >>>>>>>> >>>>>>>> Finally got hold of our KEGG data to test, and it works! >>>>>>>> >>>>>>>> Well, only on my laptop - and not the workstation, but that's a >>>>>>>> problem for tomorrow. >>>>>>>> >>>>>>>> I believe it's a setup issue, since I'm running 1.17.0 fine on my >>>>>>>> end, and Paul says 1.19.0 (the workstation version) is working. >>>>>>>> >>>>>>>> If it appears to be related I'll let everyone know. >>>>>>>> >>>>>>>> Otherwise, thank you all for your help! Our department is quite >>>>>>>> excited to get KEGG into Cytoscape! >>>>>>>> >>>>>>>> Cheers, >>>>>>>> Stuart Bradley >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Oct 11, 2013 at 7:50 AM, Paul Shannon < >>>>>>>> paul.thurmond.shannon@gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi David, >>>>>>>>> >>>>>>>>> I tried out the new code (KEGGgraph v 1.19.0), and it works great. >>>>>>>>> Thanks! >>>>>>>>> >>>>>>>>> I took the liberty (I hope you don't mind) of adding a unitTest to >>>>>>>>> your package which >>>>>>>>> >>>>>>>>> 1) fails with the old version, demonstrating Stuart's problem >>>>>>>>> 2) succeeds with the new >>>>>>>>> >>>>>>>>> The file is inst/unitTests/test_KEGGgraph.R >>>>>>>>> >>>>>>>>> - Paul >>>>>>>>> >>>>>>>>> On Oct 7, 2013, at 11:35 PM, Zhang, Jitao David wrote: >>>>>>>>> >>>>>>>>> > Dear both, >>>>>>>>> > >>>>>>>>> > I have updated KEGGgraph to version 1.18.0 (subversion >>>>>>>>> revision: 81275) in the devel branch of bioconductor. The >>>>>>>>> KEGGpathway2reactionGraph function now returns a reaction graph that can be >>>>>>>>> merged with other KEGG pathway/reaction graphs. >>>>>>>>> > >>>>>>>>> > The updated function is given below. >>>>>>>>> > >>>>>>>>> > KEGGpathway2reactionGraph <- function(pathway) { >>>>>>>>> > reactions <- getReactions(pathway) >>>>>>>>> > if(length(reactions)==0) { >>>>>>>>> > stop("The pathway contains no chemical reactions!\n") >>>>>>>>> > } >>>>>>>>> > subs <- sapply(reactions, getSubstrate) >>>>>>>>> > prods <- sapply(reactions, getProduct) >>>>>>>>> > types <- sapply(reactions, getType) >>>>>>>>> > gridlist <- lapply(seq(along=reactions), >>>>>>>>> > function(i) >>>>>>>>> > expand.grid(subs[[i]], prods[[i]], >>>>>>>>> stringsAsFactors=FALSE)) >>>>>>>>> > grid <- as.matrix(do.call(rbind, gridlist)) >>>>>>>>> > isRepGrid <- duplicated(grid) >>>>>>>>> > uniqGrid <- grid[!isRepGrid,,drop=FALSE] >>>>>>>>> > gridTypes <- rep(types, sapply(gridlist, nrow)) >>>>>>>>> > uniqGridTypes <- gridTypes[!isRepGrid] >>>>>>>>> > >>>>>>>>> > cg <- ftM2graphNEL(uniqGrid) >>>>>>>>> > allNodes <- nodes(pathway) >>>>>>>>> > allNodeNames <- sapply(allNodes, function(x) paste(getName(x), >>>>>>>>> collapse=",")) >>>>>>>>> > cgNodes <- allNodes[match(nodes(cg), allNodeNames)] >>>>>>>>> > >>>>>>>>> > cgEdges <- sapply(1:nrow(uniqGrid), >>>>>>>>> > function(x) >>>>>>>>> > new("KEGGEdge", >>>>>>>>> > entry1ID=uniqGrid[x,1], >>>>>>>>> > entry2ID=uniqGrid[x,2], >>>>>>>>> > type=uniqGridTypes[x], >>>>>>>>> > subtype=list())) >>>>>>>>> > >>>>>>>>> > ## set node and edge data - as KEGGNode and KEGGEdge >>>>>>>>> > ## attention: KEGGEdges may be more than graph edges, due to >>>>>>>>> non-genes >>>>>>>>> > names(cgEdges) <- apply(uniqGrid,1L, paste, collapse="~") >>>>>>>>> > env.node <- new.env() >>>>>>>>> > env.edge <- new.env() >>>>>>>>> > assign("nodes", cgNodes, envir=env.node) >>>>>>>>> > assign("edges", cgEdges, envir=env.edge) >>>>>>>>> > >>>>>>>>> > nodeDataDefaults(cg, "KEGGNode") <- env.node >>>>>>>>> > edgeDataDefaults(cg, "KEGGEdge") <- env.edge >>>>>>>>> > >>>>>>>>> > return(cg) >>>>>>>>> > } >>>>>>>>> > >>>>>>>>> > Try it out and please let me know if you encounter any >>>>>>>>> problem. >>>>>>>>> > >>>>>>>>> > Best wishes, >>>>>>>>> > David >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > On Tue, Sep 3, 2013 at 9:47 PM, Paul Shannon < >>>>>>>>> paul.thurmond.shannon@gmail.com> wrote: >>>>>>>>> > Hi Stuart, >>>>>>>>> > >>>>>>>>> > I have included Jitao David Zhang here as well, the package >>>>>>>>> author and maintainer. >>>>>>>>> > >>>>>>>>> > I think I can reduce your problem report to these steps: >>>>>>>>> > >>>>>>>>> > library(KEGGgraph) >>>>>>>>> > filename <- "hsa00260.kgml" >>>>>>>>> > retrieveKGML("00260", organism="hsa", destfile=filename, method >>>>>>>>> = "internal") >>>>>>>>> > pathway <- parseKGML(filename) >>>>>>>>> > >>>>>>>>> > g.reaction <- KEGGpathway2reactionGraph(pathway, uniqueReaction >>>>>>>>> = FALSE) >>>>>>>>> > g.pathway <- KEGGpathway2Graph(pathway, genesOnly=FALSE) >>>>>>>>> > >>>>>>>>> > names(nodeDataDefaults(g.reaction)) # NULL >>>>>>>>> > names(nodeDataDefaults(g.pathway)) # KEGGNode >>>>>>>>> > >>>>>>>>> > mergeKEGGgraphs (in KEGGgraph/R/graph.R) requires that there be >>>>>>>>> an edge attribute "KEGGEdge" and a node attribute "KEGGNode", and fails >>>>>>>>> with the error you saw. >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > So the reaction graph does not have the two attributes required >>>>>>>>> by mergeKEGGgraphs. I am not sure whether this is by design, or whether it >>>>>>>>> is an oversight. >>>>>>>>> > Once David clarifies that, we can devise some possible next >>>>>>>>> steps for you. >>>>>>>>> > >>>>>>>>> > - Paul >>>>>>>>> > >>>>>>>>> > P.S For future posts, please include (as I have tried to do >>>>>>>>> here) a smallish, self-contained and reproducible example, along with your >>>>>>>>> sessionInfo: >>>>>>>>> > >>>>>>>>> > R version 3.0.1 Patched (2013-05-26 r62815) >>>>>>>>> > Platform: x86_64-apple-darwin10.8.0 (64-bit) >>>>>>>>> > >>>>>>>>> > locale: >>>>>>>>> > [1] C >>>>>>>>> > >>>>>>>>> > attached base packages: >>>>>>>>> > [1] stats graphics grDevices utils datasets methods >>>>>>>>> base >>>>>>>>> > >>>>>>>>> > other attached packages: >>>>>>>>> > [1] KEGGgraph_1.17.0 graph_1.39.3 XML_3.95-0.2 >>>>>>>>> > >>>>>>>>> > loaded via a namespace (and not attached): >>>>>>>>> > [1] BiocGenerics_0.7.4 parallel_3.0.1 stats4_3.0.1 >>>>>>>>> tools_3.0.1 >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > On Sep 2, 2013, at 2:51 PM, Stuart Bradley wrote: >>>>>>>>> > >>>>>>>>> > > Hello all, >>>>>>>>> > > >>>>>>>>> > > I'm trying to build unified compound pathway maps, and have >>>>>>>>> been successful >>>>>>>>> > > using this method: >>>>>>>>> > > >>>>>>>>> > > library(graph) >>>>>>>>> > > library(KEGGgraph) >>>>>>>>> > > >>>>>>>>> > > KEGGList <- list.files(path = "C:/Users/Castor >>>>>>>>> > > Castle/Documents/kgml/metabolic/ko/subset/", full.names = TRUE) >>>>>>>>> > > >>>>>>>>> > > AllGraphs <- lapply(KEGGList, function(x) { >>>>>>>>> > > pathway <- parseKGML(x) >>>>>>>>> > > pathway <- KEGGpathway2reactionGraph(pathway, uniqueReaction >>>>>>>>> = FALSE) >>>>>>>>> > > }) >>>>>>>>> > > >>>>>>>>> > > FinalGraph <- mergeGraphs(AllGraphs, edgemode = "directed") >>>>>>>>> > > >>>>>>>>> > > However, I'd like to be able to use mergeKEGGgraphs as it >>>>>>>>> retains more >>>>>>>>> > > information. The problem is that when I replace mergeGraphs >>>>>>>>> with >>>>>>>>> > > mergeKEGGgraphs >>>>>>>>> > > I get the following error (regardless of whether it's my own >>>>>>>>> files, or the >>>>>>>>> > > example ones provided): >>>>>>>>> > > >>>>>>>>> > > Error in .verifyAttrName(attr, names(self@defaults)): >>>>>>>>> > > unknown attribute name: ŒKEGGNode‚ >>>>>>>>> > > >>>>>>>>> > > Has anyone found a work around for this? I was fiddling with >>>>>>>>> > > setKEGGnodeData/setKEGGEdgeData in conjunction with >>>>>>>>> mergeGraphs, but I >>>>>>>>> > > can't get it to work. >>>>>>>>> > > >>>>>>>>> > > Any help would be greatly appreciated. >>>>>>>>> > > >>>>>>>>> > > Cheers, >>>>>>>>> > > Stuart Bradley >>>>>>>>> > > >>>>>>>>> > > [[alternative HTML version deleted]] >>>>>>>>> > > >>>>>>>>> > > _______________________________________________ >>>>>>>>> > > Bioconductor mailing list >>>>>>>>> > > Bioconductor@r-project.org >>>>>>>>> > > https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>> > > Search the archives: >>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > -- >>>>>>>>> > >>>>>>>>> > Jitao David Zhang | 张继涛 | Computational Biology and >>>>>>>>> Bioinformatics | Pharmaceutical Divison | F. Hoffmann-La-Roche AG | CH-4070 >>>>>>>>> Basel | Switzerland >>>>>>>>> > >>>>>>>>> > Tel +41 61 688 62 51 >>>>>>>>> > >>>>>>>>> > Confidentiality Note: This message is intended only for the use >>>>>>>>> of the named recipient(s) and may contain confidential and/or privileged >>>>>>>>> information. If you are not the intended recipient, please contact the >>>>>>>>> sender and delete this message. Any unauthorized use of the information >>>>>>>>> contained in this message is prohibited. >>>>>>>>> > >>>>>>>>> > Please inform me immediately in case attached documents are >>>>>>>>> missing! >>>>>>>>> > >>>>>>>>> > >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> *Jitao David Zhang | **张继涛** | Computational Biology and >>>>>> Bioinformatics | Pharmaceutical Divison | F. Hoffmann-La-Roche AG | CH-4070 >>>>>> Basel | Switzerland***** >>>>>> >>>>>> *Tel +41 61 688 62 51 * >>>>>> >>>>>> Confidentiality Note: This message is intended only for the use of >>>>>> the named recipient(s) and may contain confidential and/or privileged >>>>>> information. If you are not the intended recipient, please contact the >>>>>> sender and delete this message. Any unauthorized use of the information >>>>>> contained in this message is prohibited.**** >>>>>> >>>>>> *Please inform me immediately in case attached documents are missing! >>>>>> * >>>>>> >>>>>> >>>>> >>>> >>> >> > > > -- > > *Jitao David Zhang | **张继涛** | Computational Biology and Bioinformatics | > Pharmaceutical Divison | F. Hoffmann-La-Roche AG | CH-4070 Basel | > Switzerland***** > > *Tel +41 61 688 62 51 * > > Confidentiality Note: This message is intended only for the use of the > named recipient(s) and may contain confidential and/or privileged > information. 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