Warning raised by extend.tree

[ArtPoon]

> phy.extend <- extend.tree(phy, seq.info, seqs, mc.cores=4, log.file="data/be.log")

Warning messages:

1: In eval(jsub, SDenv, parent.frame()) :
 NAs introduced by coercion

2: 
In annotate.growth(t, growth.info.trees, mc.cores = mc.cores) :

  Not all newly added sequences are noted in the seq.info of the tree

[ArtPoon]

I determined that this is expected behaviour associated with the root node of the tree not carrying a numeric value:

> head(t$node.label)
[1] "Root"  "0.960" "0.945" "0.827" "0.619" "0.432"

We can ignore this warning, but a more elegant workaround would be to replace Root with 1.0.

[liamxg]

[liamxg]

@ArtPoon how to solve this?

[ArtPoon]

@liamxg - Please see my question in #16

[ArtPoon]

The above problem is fixed in current development branches, closing for now.