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Hi Kaustubh, Could you also post you code so that we can try to reproduce the error? And post the result of sessionInfo() as well so that we can understand more for your machine. Thanks. Sincerely, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Tue, 20 Dec 2005, Kaustubh Patil wrote: > Dear all, > > I am using R 2.2.0 with latest releases of bioconductor and other packages (especially Rgraphviz). I am interested in drawing weighted graphs using Rgraphviz. It works perfectly fine if I change colour (color option), labels (label option) of the edge. But if I try to add weight (weight option) R exits with "segmentation fault" > > I would be grateful to have any comments. > > Thank you and Regards, > Kaustubh > > > __________________________________________________ > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

> I am using R 2.2.0 with latest releases of bioconductor and other > packages (especially Rgraphviz). I am interested in drawing weighted > graphs using Rgraphviz. It works perfectly fine if I change colour > (color option), labels (label option) of the edge. But if I try to add > weight (weight option) R exits with "segmentation fault" Could you please describe in more detail exactly what you're doing here? Plotting w/ edge weights in a standard manner works for me here, but that doesn't mean I'm doing the same thing you are.

Dear Kaustubh, thanks for reporting. In order for this report to be useful and for anyone to be able to do anything about this, we need a code example to reproduce the problem. I could imagine this is a real bug, but unless somebody else can reproduce it, it could also be caused by anything else, including cosmic rays or bad feng shui in your computer room. Cheers Wolfgang Kaustubh Patil wrote: > Dear all, > > I am using R 2.2.0 with latest releases of bioconductor and other packages (especially Rgraphviz). I am interested in drawing weighted graphs using Rgraphviz. It works perfectly fine if I change colour (color option), labels (label option) of the edge. But if I try to add weight (weight option) R exits with "segmentation fault" > > I would be grateful to have any comments. > > Thank you and Regards, > Kaustubh > > __________________________________________________ > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber

Dear Kaustubh, Just an idea... I've never used Rgraphviz, but I've had similar problems in RGBL with graphs which have negative weights (already reported on the list). Have you checked that the weights you're trying to add are positive? Cheers Adrien > Dear Kaustubh, > > thanks for reporting. In order for this report to be useful > and for anyone to be able to do anything about this, we need > a code example to reproduce the problem. I could imagine this > is a real bug, but unless somebody else can reproduce it, it > could also be caused by anything else, including cosmic rays > or bad feng shui in your computer room. > > Cheers > Wolfgang > > > Kaustubh Patil wrote: > > Dear all, > > > > I am using R 2.2.0 with latest releases of bioconductor > and other packages (especially Rgraphviz). I am interested in > drawing weighted graphs using Rgraphviz. It works perfectly > fine if I change colour (color option), labels (label option) > of the edge. But if I try to add weight (weight option) R > exits with "segmentation fault" > > > > I would be grateful to have any comments. > > > > Thank you and Regards, > > Kaustubh > > > > > __________________________________________________ > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- > Best regards > Wolfgang > > ------------------------------------- > Wolfgang Huber > European Bioinformatics Institute > European Molecular Biology Laboratory > Cambridge CB10 1SD > England > Phone: +44 1223 494642 > Fax: +44 1223 494486 > Http: www.ebi.ac.uk/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Hi Li, It has to do with the sp.between function. Here is the thread where I reported the bug: https://stat.ethz.ch/pipermail/bioconductor/2005-November/011066.html Hope that helps, Adrien > > Hi, Adrien, > > Could you be a bit more specific about the problem(s) you > encounter in RBGL? > Some algorithms in RBGL only handle graphs with positive > weights, while others could take both positive AND negative > weights. If an algorithm fails to do what it's supposed to > do, I'd like to know about it and try to fix it (or document > it more clearly). > > Thanks > > Li > > > > > Dear Kaustubh, > > > > Just an idea... I've never used Rgraphviz, but I've had similar > > problems in RGBL with graphs which have negative weights (already > > reported on the list). > > > > Have you checked that the weights you're trying to add are positive? > > > > Cheers > > Adrien > > > >

> But how do I do that? Look at the man page for addEdge, there is a mechanism for adding weights on edge creation. BTW, I checked in a fix for this problem, Rgraphviz version 1.9.2.