Re: [igraph] At structure_generators.c:84 : Invalid (negative) vertex id, Invalid vertex id

[Stephan Schlögl]

Hi Federik,
Thank you very much for your help. The error message was a bit 
missleading. I didn't even think of this problem. But you where right my 
graph wasn't really bipartite I had an error in my script. Here is a bit 
faster snippet to identify the problematic edges:

e <- get.data.frame(g,what="edges")
v <- get.data.frame(g,what="vertices")
e$from_type <- v$type[match(e$[,1],v$name)]
e$to_type <- v$type[match(e[,2],v$name)]
e[e$from_type==e$to_type,]

by the way: In this case the projections result in a graph with v=54183 
e=266112529 and one which is  v=135 e=8044. I'am just interested in the 
second projection which is much smaller. Is there a way to just compute 
the second one and would this save computational ressources?

Best,
stephan




Am 2013-11-25 18:00, schrieb Frederik Elwert:
> Hello Stephan,
>
> there were some issues like this on the list: It seems like the error
> message is a red herring, and the actual problem is with the
> bipartiteness of your graph. I suggested a simple test, and it shows
> some issues:
>
> > for (v in V(G)) {
> +     vtype <- V(G)[v]$type
> +     for (n in neighbors(G, v)) {
> +         if (V(G)[n]$type == vtype) {
> +             print(paste('Problem with', V(G)[v]$name, 'and',
> V(G)[n]$name))
> +         }
> +     }
> + }
> [1] "Problem with 1276601 and 444969570"
> [1] "Problem with 1417761 and 444969570"
> [1] "Problem with 1600201 and 444969570"
> [1] "Problem with 1612811 and 444969570"
> [1] "Problem with 1999731 and 444969570"
> [1] "Problem with 6467932 and 444969570"
> [1] "Problem with 8179472 and 444969570"
> [1] "Problem with 8507372 and 444969570"
> [1] "Problem with 8560922 and 444969570"
> ...
>
> So maybe you should double-check your graph is bipartite according to
> your "type" attribute. (As I learned here, is.bipartite(g) only checks
> if the graph is bipartite according to *any* mapping.) Checking the type
> of node 444969570 might be a good start. (I couldn’t test a fixed
> mapping, as my machine runs out of memory with bipartite.projection on
> your graph.)
>
> Regards
> Frederik
>
>
>
> Am 25.11.2013 17:45, schrieb Stephan Schlögl:
> > Hi,
> > I'm using igraph in R. I'm trying to compute:
> >
> > /graph <-bipartite.projection(g)/
> >
> > but I get the following error:
> >
> > /At structure_generators.c:84 : Invalid (negative) vertex id, Invalid
> > vertex id/
> >
> > this seems strange to me because I'm not using negative vertex ids.
> >
> > /> min(V(g)$name)//
> > //[1] "100000090"/
> > /#(not sure if this is the correct way to prove this, since $name seems
> > to be a string)/
> >
> > I suppose the only way to make this reproducible is by providing the
> > graph object <http://homepage.univie.ac.at/stephan.schloegl/net.RData>
> >
> > I would gratefull for any help!
> > Best,
> > stephan
> >
> >
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