[Phylobase-devl] getting close!

Ben Bolker bolker at ufl.edu
Fri Aug 21 21:51:32 CEST 2009

  still aiming for next Friday.  I would like to close all current bugs
if possible.

  * no significant warnings in current build (thanks to François
for cleaning up the docs).  Can we close #590?

  * build is still failing on MacOS, somehow I failed to disable
Wno-long-double; could someone else take a look?  then, if the binary
works on OS X 10.4, we can close #269

  * #547, non-unique labels: François?  is this just a matter of
commenting out a test or two and making sure nothing obvious breaks?

  * questions about subset(): is the intention that exactly ONE of
(tips.include, tips.exclude, mrca, node.subtree) be specified?  (That
seems to make sense -- sorting out conflicts among the options would be
a nightmare.)  I am about to commit a fix for #595 (it is a moderately
radical internal restructuring of subset(), but doesn't seem to break
testprune.R or make the examples do anything silly ...)

  * #589: do this, or move it to "feature request/enhancement"?


  * #120: ("add a convenient way to bind data to phylo4d objects")
close?  do we think there are still any dangerous corners poking out
of the way we handle tdata<-, or did that get resolved?

  * #175-176: should I go ahead and add two list() slots to the
phylo4(d) classes for metadata/annotation?

  * #570: Steve?  did you plan on implementing the ape-translation
hack for root node replacement?

  * #557: I have started on this, will e-mail separately about it.

  * in addition, anyone who can should poke around in the documentation
looking for bad things.  It might be particularly helpful to get
non-participants in the latest hackathon to do this ...

  * do people have strong feelings about NEWS vs ChangeLog formats?
I think we should include at least one.


  see also <http://arthurdejong.org/svn2cl/>


Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bolker at ufl.edu / www.zoology.ufl.edu/bolker
GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc

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