[Phylobase-devl] anyone there?

Ben Bolker bolker at ufl.edu
Thu Aug 20 18:30:07 CEST 2009

  I know we have gone well beyond our original plan in terms of time &
effort (although I think it has been very valuable) -- people may now
have lives they need to get back to (there's this ms. I ought to finish
revising, and classes start next week ...)

  Are people planning on working today/in the near future?  Being on IRC?

  What do people think about release plans?

  I would say we have:

1. rooting issues (bugs #423 ...) (Kimbel, Michonneau?)

    we could probably implement replacing the root node via


   and close out the bug/add the functionality, but if Steve/Peter
   are close to having a native solution, that would be better ...

   what else do we want/need?  should  rootNode(x) <- NA produce
   an unrooted tree?

2. labeling issues (bugs #547)

   we also have a minor issue in the output of misctests.R , which
now includes:

> Note: Method with signature "phylo4d#missing#ANY" chosen for function
>  target signature "phylo4d#missing#character".
>  "phylo4#ANY#character" would also be valid
> Note: Method with signature "phylo4#character" chosen for function
>  target signature "phylo4d#character".
>  "phylo4d#ANY" would also be valid

  it would be nice to clean this up, but if we understand it perhaps
we could ignore it instead.

3. build issues (#269 -- maybe closed?; I propose that #554, #583 get
   downgraded or become "features")

   we still have Mac build problems on r-forge: now it's

cc1plus: error: unrecognized command line option "-Wno-long-double"
make[2]: *** [nxsassumptionsblock.lo] Error 1
make[1]: *** [all-recursive] Error 1

  should we just hack -Wno-long-double out of the make/config files and
hope for the best??

  is there any chance we can dispense with the UTF-8 encoding?
The R extensions manual (p. 32) is pretty pessimistic about this.
And we get a warning on R-forge:

 Rd warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is
not possible

4. plotting: none, really. #568 should be closed.  I really really want
a plotting option other than bubbles, but that's an enhancement rather
than a bug.

5. misc/cleanup: #590.  #575?
   also, make sure all doc warnings are cleaned up.

6. testing (#589): finish moving tests to RUnit framework??  what is the
    status?  I need someone to explain a little more to me about how
    this works, I have questions ... is a complete move to RUnit
necessary for release?

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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