[BioC] Problems with combineNodes in graph

[Florian Hahne]

Hi Michael,
this was a bug in the graph package which should now be fixed in the 
latest devel version (1.21.5)
I also fixed the bug in edgeWeights which will now correctly return an 
empty list for all nodes in index instead of a list for all nodes of the 
whole graph, in the boundary case of a graph without any edges.

Thanks for pointing this out,
Florian

Michael Hahsler wrote:
> Hi,
>
> I encountered the following problem with the package graph. Maybe 
> someone can tell me what I'm doing wrong.
>
>
> > library("graph")
> >
> > sessionInfo()
> R version 2.8.1 (2008-12-22)
> i486-pc-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] graph_1.20.0
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.12 tools_2.8.1
> >
> > g <- new("graphNEL", nodes = as.character(1:10), edgemode="directed")
> > g <- addEdge("1", "10", g, 1)
> > combineNodes(as.character(1:5), g, "1")
> Error in graph:::.normalizeEdges(from, to) :
>   'from' must be length 1 or 1 for this call.
> >
> > combineNodes(c("1","2"), g, "X")
> Error in graph:::.normalizeEdges(from, to) :
>   'from' must be length 1 or 1 for this call.
>
>
> Thanks,
> Michael
>


-- 
Florian Hahne, PhD
Computational Biology Program
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-3148
fhahne at fhcrc.org