Hello Martin,

  Below is a reduced version of our code that doesn't produce an error in
r61643 but does in 2.15.2.

  Thanks,
  -- François

setClass("phylo4",
         representation(edge="matrix",
                        annote="list"),
         prototype = list(edge = matrix(nrow = 0, ncol = 2),
                        annote = list())
)

setGeneric("phylo4", function(x, ...) { standardGeneric("phylo4")} )

setMethod("phylo4", "matrix",
    function(x, annote = list()) {
    res <- new("phylo4")
        res@edge <- x
        res@annote <- annote
        res
    }
)

edge <- structure(c(6L, 7L, 8L, 8L, 9L, 9L, 7L, 6L, 7L, 8L, 1L, 9L,
      2L, 3L, 4L, 5L), .Dim = c(8, 2))
phylo4(edge, annote="foo")




On Mon, Jan 14, 2013 at 1:39 PM, Martin Maechler <maechler@stat.math.ethz.ch
> wrote:

> phylo4 <- setClass("phylo4",
>          representation(edge = "matrix",
>                         edge.length = "numeric",
>                         label = "character",
>                         edge.label = "character",
>                         order = "character",
>                         annote = "list"),
>          prototype = list(edge = matrix(nrow = 0, ncol = 2,
>                                         dimnames = list(NULL,
>                                         c("ancestor", "descendant"))),
>                           edge.length = numeric(0),
>                           label = character(0),
>                           edge.label = character(0),
>                           order = "unknown",
>                           annote = list()
>          )
>

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