[Phylobase-devl] anyone there?

[Peter D. Cowan]

On Thu, Aug 20, 2009 at 12:30:07PM -0400, Ben Bolker wrote:
> 
>   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
> 
>    as(ape::root(as(x,"phylo"),value),"phylo4")
> 
>    and close out the bug/add the functionality, but if Steve/Peter
>    are close to having a native solution, that would be better ...

I think we are well on our way to a native solution, but unless Steve wants to take a crack at it, I think it will have to wait.

>    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
> "labels<-",
> >  target signature "phylo4d#missing#character".
> >  "phylo4#ANY#character" would also be valid
> 103a101,103
> > Note: Method with signature "phylo4#character" chosen for function
> "nodeLabels<-",
> >  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.

What did you have in mind for the plotting things.  There are other options, but not default (or too easy at the moment).

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

I said doc warnings and the minimal docs (filled in to avoid the warnings), are probably the biggest task left.

> 
> 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?
> 

None of the RUnit tests are not necessary for a release.  From my point of view they are nicer than the other testing frameworks for a few reasons.  For one there is a nice output, if you look in the unitTests folder of the built package it contains the report.html file which is a summary of all the tests.  It's also nice because the tests will continue even if one fails and they can be run w/o R check, which reduces the iteration.  Lastly you can deactivate some tests, if you know for instance that they will fail and don't want to run them yet.  

> -- 
> 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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