[BioC] bugfix in graph::ftM2graphNEL

[Wolfgang Huber]

Dear List,

Thanks to Dan Bebber for pointing out a bug in the function ftM2graphNEL
in the "graph" package and to Seth for help with fixing it. Those who
use this function should update to version 1.12.1 in the release branch
http://www.bioconductor.org/packages/1.9/bioc/html/graph.html
or version 1.13.6 in the development branch.

The bug is a lesson on "beware of partial matching when accessing list
elements by name":

x = list(foobar="lemon")
x[["a"]]
#   NULL
x[["f"]]
#   [1] "lemon"

But

x = list(foobar="lemon", f="plum")
x[["f"]]
#   [1] "plum"

and as a result, edges in the graph were invented if there were nodes
with no out-edges whose name partially matched the name of other
nodes with out-edges.

  Best wishes
  Wolfgang


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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber