The first was that I had inadvertently corrupted an S3 method
multi2di of ape when I created the function
multi2di.simmap without exporting a method to the namespace. The
other issues came up in
R CMD check and included such things
as failing to import various functions from dependencies, other problems with
the namespace, errors in documenting various variables, the absence of a manual
page for one function (
likSurface.rateshift) that is exported
by phytools, and a few problems with the R code of some new functions.
I too hope to update the version of phytools on CRAN as the current version dates to June.
The latest phytools version can be installed from GitHub using devtools as follows:
Since both phangorn & ape are in the process of being updated, but phytools depends on the latest version of neither, you may need to do: