[Phylobase-devl] release date

Jim Regetz regetz at nceas.ucsb.edu
Thu Aug 27 18:37:09 CEST 2009

I agree the recent progress has been great! I also agree with Peter's 
sentiment, and am partial to François' second alternative: holding off a 
little longer on the CRAN release to address these issues and others 
that arise as we're working (we don't seem to have reached an asymptote 
yet), but making an immediate announcement on R-sig-phylo to draw more 
attention to the package on R-Forge. This should expand the user (and 
thus tester) base, while still limiting it to folks who can be expected 
to tolerate some ongoing changes and imperfect functionality in places.

As I see it, this would be the 'beta' version of the 'alpha' 
announcement Ben posted to r-sig-phylo in Feb 2008. And this would 
certainly follow a precedent set by the 'sp' package, which has 
successfully done for the r-spatial realm what phylobase is intended to 
do for r-phylo.


With regard to the subsetting/pruning problem, it's not just that it 
doesn't work in some cases, but it actually produces the wrong answer. 
And at least in my usage, subsetting is a core tree operation that I 
would really expect to work properly in phylobase.

IMHO François' road map is a good road map to CRAN, coupled with fixing 
any important bugs that we might come across in the process. The release 
certainly doesn't have to be totally feature rich and flawless, but 
making sure the core functionality is rock solid is important. Releasing 
*tomorrow* seems a bit rushed for my tastes. First impressions can be 
lasting! There are certainly R packages on CRAN that I've installed 
once, been unimpressed with, and never tried again...


François Michonneau wrote:
> Hi,
>   I think we should still plan of releasing it. My main concern is that
> if we don't, we won't keep the pace we have been having in the last
> couple of weeks, and the official release will be delayed. If people do
> start using it, then they will report bugs (not too many I hope) and
> keep development going.
>   However, I agree there is still some polishing to do before officially
> releasing it. It would be valuable to identify what are the things that
> we really need to change before the release. In my opinion, one of main
> things is that we need to use consistent variable names for
> phylo4/phylo4d in our functions. They are currently called: x, phy,
> object, etc. I can imagine that it's confusing for new users reading the
> documentation. This is important to do before the release because if we
> harmonize these names in the future, we can break people code if they
> use explicit variable names in their calls.
>   I agree that it would be nice to have our own subsetting and rerooting
> functions. At this stage, however, it seems to me OK to release
> phylobase even if these 2 functions don't work. Most other aspects of
> phylobase are functional and should allow people to start working with
> it.
>   Because these functions don't work and yet are important, we should
> however probably release phylobase as a beta-1 version. Meanwhile, we
> should think about a road map with our objectives for the future
> releases. I propose that we use the 0.4 release series as beta, and have
> 0.5 series as the first official release.
> * beta-2 (0.4.2): non-unique labels, subsetting, rerooting
> * beta-3 (0.4.3): methods for multiPhylo4 and multiPhylo4d, no
> dependencies from APE, identify method
> * rc-1 (0.4.4): all functions have RUnit tests
> * rc-2 (0.4.5): complete documentation and vignettes
>   Alternatively, if we decide to not release quite yet on CRAN, we can
> just send out announcements to the R-phylo mailing list and ask people
> to test phylobase (from R-forge) and get their feedback.
>   Cheers,
>   -- François
> On Wed, 2009-08-26 at 23:00 -0700, Peter D. Cowan wrote:
>> This might be verboten to even suggest, but should we push off the release date?  In the last month we've made a 150 commits to phylobase, that's pretty awesome.  If we can keep up even a portion of this momentum, it may be worth while to hold off on releasing the package until we can finish a few things off.  Or, if we don't see ourselves having time at the moment, we can release as planned on Friday, and address the issues we've identified in a "Known Issues" section, and try to organize a 0.5.1 release down the road.
>> Top on my list would be replacing our two ape dependencies.  The rerooting and subsetting are not trivial things to write, but the process of calling out to ape seems not to work the way we had hoped.  Unfortunately, I won't have time to do this until next week sometime.  
>> Cheers
>> Peter
>> _______________________________________________
>> Phylobase-devl mailing list
>> Phylobase-devl at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl
>> ------------------------------------------------------------------------
>> _______________________________________________
>> Phylobase-devl mailing list
>> Phylobase-devl at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl

More information about the Phylobase-devl mailing list