[Phylobase-devl] getting close!

Peter D. Cowan pdc at berkeley.edu
Sat Aug 22 00:17:25 CEST 2009

On Fri, Aug 21, 2009 at 03:51:32PM -0400, Ben Bolker wrote:
>   still aiming for next Friday.  I would like to close all current bugs
> if possible.

I think both of these are good/doable goals.

>   * no significant warnings in current build (thanks to François
> for cleaning up the docs).  Can we close #590?
>   * build is still failing on MacOS, somehow I failed to disable
> Wno-long-double; could someone else take a look?  then, if the binary
> works on OS X 10.4, we can close #269

I've made a change to remove another instance of Wno-long-double, it builds on my mac, but so did the earlier revisions.  Hopefully, no more 24 hour iterations...

>   * #547, non-unique labels: François?  is this just a matter of
> commenting out a test or two and making sure nothing obvious breaks?
>   * questions about subset(): is the intention that exactly ONE of
> (tips.include, tips.exclude, mrca, node.subtree) be specified?  (That
> seems to make sense -- sorting out conflicts among the options would be
> a nightmare.)  I am about to commit a fix for #595 (it is a moderately
> radical internal restructuring of subset(), but doesn't seem to break
> testprune.R or make the examples do anything silly ...)
>   * #589: do this, or move it to "feature request/enhancement"?

In an ideal world a lack of tests would be a bug, but we'd have a long bug list if we stuck to that.  I'm fine with deferring this.

>   Features
>   * #120: ("add a convenient way to bind data to phylo4d objects")
> close?  do we think there are still any dangerous corners poking out
> of the way we handle tdata<-, or did that get resolved?
>   * #175-176: should I go ahead and add two list() slots to the
> phylo4(d) classes for metadata/annotation?

I thought there was something more complicated in the offing for metadata?  If so I'd say wait until that is ready.

>   * #570: Steve?  did you plan on implementing the ape-translation
> hack for root node replacement?
>   * #557: I have started on this, will e-mail separately about it.

Great, this is a personal favorite of mine!

>   * in addition, anyone who can should poke around in the documentation
> looking for bad things.  It might be particularly helpful to get
> non-participants in the latest hackathon to do this ...
>   * do people have strong feelings about NEWS vs ChangeLog formats?
> I think we should include at least one.
> <http://www.gnu.org/prep/standards/standards.html#NEWS-File>,
> <http://www.gnu.org/prep/standards/standards.html#Change-Logs>
>   see also <http://arthurdejong.org/svn2cl/>

It seems to me that the NEWS file is more useful.  Anyone interested in every change could run svn log.  NEWS files also seem to be expected in R packages (according to R-ext).  Supposedly the R function news() should interface w/ news files, but I wasn't able to get it to work.


>    cheers
>      Ben
> -- 
> 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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