[Phylobase-devl] anyone there?
Peter D. Cowan
pdc at berkeley.edu
Thu Aug 20 19:57:37 CEST 2009
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
> 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
> > 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: *** [nxsassumptionsblock.lo] Error 1
> make: *** [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
> Phylobase-devl mailing list
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