[Phylobase-devl] anyone there?

[Brian O'Meara]

On Aug 20, 2009, at 1:13 PM, François Michonneau wrote:

> 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.

I moved #554 to a feature.

>
>>   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].

I just successfully built the latest phylobase from source on Macs  
running 10.4 and 10.5. However, I'm using gcc 4.0.1 on both 10.5 and  
10.4, and R-forge is using gcc 4.2.1. I remember some other code (not  
phylobase) breaking with new versions of gcc -- perhaps this is the  
same thing. Do we know which gcc CRAN uses? I suspect removing the - 
Wno-long-double would be fine (we don't really do anything using the  
NCL code that would be affected by numerical precision (unless people  
have really precise character values).

>
>>  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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________________________________________________
Brian C. O'Meara
Asst. Prof., Dept. of Ecology and Evolutionary Biology
University of Tennessee, Knoxville
http://www.brianomeara.info
865-408-TREE (8733)