[BioC] Package "graph": bug in function addEdge

[Dirk Koschützki]

Dear Seth,

thanks for your detailed reply.

On 4/11/07, Seth Falcon <sfalcon at fhcrc.org> wrote:
>  [..]

> We also found that many methods for manipulating and computing on
> graphs made assumptions that failed when the input graph was
> non-simple.  So it isn't quite true that non-simple graphs were
> supported in earlier versions -- they were tolerated ;-)

I see your point but one thing is bad(*) in the way it was done: It
breaks old code. It took me several days to trace a wrong result in my
code back to the changed behaviour of the graph package. Therefore I
would deeply recommend to add something like a warning or a specific
fragment of deprecation in such a situation.

(*) By bad I mean not only my personal situation but in the sense of
the "design by contract" principle. The package worked with
multigraphs, therefore it either has to do it forever or explicitly
"cancel the contract" in the sense of issuing a warning or the like.
Otherwise situations like this might happen often over time.

> We don't have the resources, or use-cases, right now to implement
> classes for multigraphs or other non-simple graphs.  But we would
> welcome well-written patches to the graph package that added such
> support.  Extending graphNEL and providing specialized methods for
> addEdge, removeEdge might be a start.

I see your point but right now I can not help with that as I have to
finish writing a thesis...

Again, thanks for the great software and all the work done.

All the best,
Dirk