[Phylobase-devl] anyone there?

François Michonneau francois.michonneau at gmail.com
Thu Aug 20 19:13:38 CEST 2009

On Thu, 2009-08-20 at 12:30 -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")

I think it's what Steve wanted to do... 

>    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
> "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.

I think we don't have this issue anymore. The message comes from the
difference between the output and misctests.Rout.save. At least, if I
source misctests.R the message about the signature choices doesn't show
up. Ben, can you confirm this?

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

I am ok with this.

>    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??

We can... but it would be best if someone with a Mac can try to figure
it out. [It seems frustrating to rely on R-forge builds].

>   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

I included the UTF-8 encoding to have my first corrected displayed. I'm
going to remove it.

> 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.

I think I'm just going to go ahead and create the option I suggest in
the bug. It shouldn't take long at all to fix.

> 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?

It seems to me that Jim pushed most of the changes last night. He moved
my tests to the correct directory.
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