[BioC] can't get degree function to work in graph package

[Paul Shannon]

Hi Burak,

You turned up a very odd bug.  And a mysterious one.

I just looked at the unit tests for degree, and they do not include exactly the case you used:  a graphNEL returned by the randomEGraph method.  But degree is successfully called on graphNEL's, and those tests run every day.  Puzzling.

Could you send me your g1 as an RData object?  

- Paul


On Mar 12, 2012, at 10:29 AM, Burak Kutlu wrote:

> Hello
> I am trying to call 'degree' on a graphNEL object and I get the following error using the example from the vignette. 
> Thanks for your help
> -burak
> 
>> library(graph)
>> set.seed(123)
>> g1 = randomEGraph(LETTERS[1:15], edges=100)
>> g1
> A graphNEL graph with undirected edges
> Number of Nodes = 15 
> Number of Edges = 100 
>> 
>> 
>> nodes(g1)
> [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O"
>> degree(g1)
> Error in degree(g1) : Not a graph object
>> 
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
> [7] LC_PAPER=C                 LC_NAME=C                 
> [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] igraph_0.5.5-4        RBGL_1.30.1           org.Mm.eg.db_2.6.4   
> [4] RSQLite_0.11.1        DBI_0.2-5             AnnotationDbi_1.16.18
> [7] Biobase_2.14.0        graph_1.32.0          BiocInstaller_1.2.1  
> 
> loaded via a namespace (and not attached):
> [1] IRanges_1.12.6 tools_2.14.1  
>> 
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> 
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