When I access one of my graph objects, using graph 1.18.1, I am encouraged to run 'updateGraph': > g.greenblatt A graphNEL graph with directed edges Number of Nodes = 3672 Number of Edges = 28634 Warning messages: 1: The edgemode slot is deprecated. Use 'updateGraph' to update this graph object. 2: The edgemode slot is deprecated. Use 'updateGraph' to update this graph object. So I try to do so, assuming (first) that my graphNEL will be modified in place > updateGraph (g.greenblatt) A graphNEL graph with directed edges Number of Nodes = 3672 Number of Edges = 28634 Warning messages: 1: The edgemode slot is deprecated. Use 'updateGraph' to update this graph object. 2: The edgemode slot is deprecated. Use 'updateGraph' to update this graph object. But no luck. I still get the warning: > g.greenblatt A graphNEL graph with directed edges Number of Nodes = 3672 Number of Edges = 28634 Warning messages: 1: The edgemode slot is deprecated. Use 'updateGraph' to update this graph object. 2: The edgemode slot is deprecated. Use 'updateGraph' to update this graph object. Just to be sure, I test the possibility that updateGraph returns an updated copy. It seems so, but the warning is still present: > g.greenblatt.new = updateGraph (g.greenblatt) > g.greenblatt.new A graphNEL graph with directed edges Number of Nodes = 3672 Number of Edges = 28634 Warning messages: 1: The edgemode slot is deprecated. Use 'updateGraph' to update this graph object. 2: The edgemode slot is deprecated. Use 'updateGraph' to update this graph object. Any advice? Thanks - - Paul

try this g.greenblatt = updateGraph (g.greenblatt) On Tue, Jul 1, 2008 at 8:03 PM, Paul Shannon <pshannon@systemsbiology.org> wrote: > When I access one of my graph objects, using graph 1.18.1, I am encouraged > to > run 'updateGraph': > > > > g.greenblatt > A graphNEL graph with directed edges > Number of Nodes = 3672 > Number of Edges = 28634 > Warning messages: > 1: The edgemode slot is deprecated. Use 'updateGraph' to update this > graph object. > 2: The edgemode slot is deprecated. Use 'updateGraph' to update this > graph object. > > So I try to do so, assuming (first) that my graphNEL will be modified in > place > > > updateGraph (g.greenblatt) > A graphNEL graph with directed edges > Number of Nodes = 3672 > Number of Edges = 28634 > Warning messages: > 1: The edgemode slot is deprecated. Use 'updateGraph' to update this > graph object. > 2: The edgemode slot is deprecated. Use 'updateGraph' to update this > graph object. > > But no luck. I still get the warning: > > > g.greenblatt > A graphNEL graph with directed edges > Number of Nodes = 3672 > Number of Edges = 28634 > Warning messages: > 1: The edgemode slot is deprecated. Use 'updateGraph' to update this > graph object. > 2: The edgemode slot is deprecated. Use 'updateGraph' to update this > graph object. > > Just to be sure, I test the possibility that updateGraph returns an updated > copy. > It seems so, but the warning is still present: > > > g.greenblatt.new = updateGraph (g.greenblatt) > > g.greenblatt.new > A graphNEL graph with directed edges > Number of Nodes = 3672 > Number of Edges = 28634 > Warning messages: > 1: The edgemode slot is deprecated. Use 'updateGraph' to update this > graph object. > 2: The edgemode slot is deprecated. Use 'updateGraph' to update this > graph object. > > Any advice? > > Thanks - > > - Paul > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]