[BioC] bug in graph::removeEdge() on UGs with graphBAM objects

[Robert Castelo]

hi,

i've come across the following bug in the 'graph' package related to the 
method 'removeEdge()' for 'graphBAM' objects:

library(graph)

g <- graphBAM(data.frame(from="A", to="B", weight=1))

g
A graphBAM graph with undirected edges
Number of Nodes = 2
Number of Edges = 1

edges(g)
$A
[1] "B"

$B
[1] "A"


removeEdge(from="A", to="B", g=g)
A graphBAM graph with undirected edges
Number of Nodes = 2
Number of Edges = 0


up to here everything is fine, the problem shows up when i try to remove 
this undirected edge swapping the values of the 'from' and 'to' argument 
because then the edge is not removed, even though the graph is 
undirected, and therefore, is that it should work in this case either way:

removeEdge(from="B", to="A", g=g)
A graphBAM graph with undirected edges
Number of Nodes = 2
Number of Edges = 1


and in fact it does work if the input 'graphBAM' object is coerced to a 
'graphNEL' or a 'graphAM' object:

removeEdge(from="B", to="A", g=as(g, "graphNEL"))
A graphNEL graph with undirected edges
Number of Nodes = 2
Number of Edges = 0

removeEdge(from="B", to="A", g=as(g, "graphAM"))
A graphAM graph with undirected edges
Number of Nodes = 2
Number of Edges = 0

this can be reproduced both in release and devel; see my sessionInfo() 
below for both cases.


best regards,

robert.
ps1: sessionInfo() ## release
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C 
LC_TIME=en_US.UTF8
  [4] LC_COLLATE=en_US.UTF8     LC_MONETARY=en_US.UTF8 
LC_MESSAGES=en_US.UTF8
  [7] LC_PAPER=en_US.UTF8       LC_NAME=C                 LC_ADDRESS=C 

[10] LC_TELEPHONE=C            LC_MEASUREMENT=en_US.UTF8 
LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] graph_1.42.0   vimcom_0.9-93  setwidth_1.0-3 colorout_1.0-2

loaded via a namespace (and not attached):
[1] BiocGenerics_0.10.0 parallel_3.1.0      stats4_3.1.0 
tools_3.1.0

ps2: sessionInfo() ## devel
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C 
LC_TIME=en_US.UTF8
  [4] LC_COLLATE=en_US.UTF8     LC_MONETARY=en_US.UTF8 
LC_MESSAGES=en_US.UTF8
  [7] LC_PAPER=en_US.UTF8       LC_NAME=C                 LC_ADDRESS=C 

[10] LC_TELEPHONE=C            LC_MEASUREMENT=en_US.UTF8 
LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] graph_1.43.0   vimcom_0.9-93  setwidth_1.0-3 colorout_1.0-2

loaded via a namespace (and not attached):
[1] BiocGenerics_0.11.3 parallel_3.1.0      stats4_3.1.0 
tools_3.1.0