[Phylobase-devl] Aug. virtual hackathon

Peter D. Cowan pdc at berkeley.edu
Sun Aug 16 00:46:29 CEST 2009


On Thu, Aug 13, 2009 at 11:41:19AM -0400, François Michonneau wrote:
> Hi all -
> 
>   I just committed the last changes in my branch and a PDF document [1]
> that describes what I have been doing on my branch. I wrote it fairly
> quickly, so I hope there aren't too many mistakes.

[From the PDF]
|Tip and internal node labels have now internal names that are simply the node 
|they are supposed to document. It thus becomes possible to store labels in any 
|order and it makes assignment of labels more robust.

I'm going to play devils advocate (and profess ignorance) here, what problem does this address?  How was label assignment non-robust before?  Was it an issue of bugs, or was there a design flaw?

Also what changes might need to be made to other code, specifically do you think I'll need to update the plotting code to handle the new label system?

|The user can however provide a named vector (the names being the node numbers), 
|in which case, the labels will be matched. 

For me the difficulty with all of the node naming issues is keeping track of/figuring out which node number I want to change.  It seems in a case where the nodes already have a name I would want to match that if possible.  If I already have a node name and I want to change it, do I need to figure out the node number first, or can I use the node name that already exists?

If no one is opposed to integrating these changes we should consider doing it before, or at the beginning of the sessions, so that we're all working with the most up-to date version.  I can help with merging if there are any questions.

[snip]

>   It builds without the vignette (R CMD build fm-branch --no-vignettes).
> It doesn't check however, but I don't think it's related to my changes
> as it fails with the following error message:
> * checking PDF version of manual without index ... ERROR
> It looks that it comes from a typo in the vignette. I'll try to
> investigate the problem.

We should also note that the latest versions of R-devel (2.10), have changed the way docs are built and checked.  Specifically there is not support in R check for documentation of S4 classes and methods.  R check w/ devel reports at least a couple more documentation warnings than it did before.  I'm going to try to get an automated R check running before the hackathon, hopefully with an R daily.

Peter

>   Concerning the hackathlon, Aug 18th, 11am EDT works for me.
> 
>   Concerning what needs to be done during the hackathlon, I'd prefer to
> use the tracker this time instead of the wiki.
> 
>   Feel free to ask questions about the document or the changes I made in
> my branch.
> 
>   Cheers,
>   -- François
> 
> [1] you can find it at www/misc/fm-branch.pdf in the subversion tree
> 
> 
> 
> On Thu, 2009-08-13 at 11:01 -0400, Ben Bolker wrote:
> > I would also prefer not a weekend (but not impossible either).
> > 
> >   Just to start the ball rolling, I propose Tuesday August 18
> > at 11 AM EDT (a little early for west-coast folks, but not
> > horrendous -- since Marguerite
> > can't play right now, we don't have to worry about Hawai'i)
> > 
> >   ??
> > 
> >   cheers
> >     Ben
> > 
> > Peter Cowan wrote:
> > > If I gather correctly, most folks are available after the 13th and  
> > > before the 24th, except for Thibaut who is currently far away from a  
> > > computer.
> > > 
> > > What days in that period work best?  Last time did we schedule it over  
> > > a weekend, or did it just feel like that because I was traveling?  I  
> > > prefer it not be a weekend, but can do it if need be.  Proposals for a  
> > > specific starting day and duration welcome.
> > > 
> > > Before, we actually start coding, it's probably worthwhile having at  
> > > least some discussion about the changes that Francois has made, and  
> > > any other major changes people would like.  It would also be good to  
> > > get the RUnit stuff checked in (if I can help at all with that let me  
> > > know Jim) so that we can make a good dent in writing unit tests (which  
> > > will make any future changes much easier to carry out).
> > > 
> > > Cheers
> > > 
> > > Peter
> > > 
> > > On Aug 3, 2009, at 4:48 PM, Marguerite Butler wrote:
> > > 
> > >> Hi Folks,
> > >>
> > >> This does sound great. Some of the students I've worked with would  
> > >> really appreciate a more stable package that was also easier to  
> > >> install.
> > >>
> > >> But I won't be able to participate this time. Need to work on my  
> > >> tenure packet (ugg) and upcoming classes.
> > >>
> > >> Marguerite
> > >>
> > >> On Aug 3, 2009, at 11:11 AM, Jim Regetz wrote:
> > >>
> > >>> This sounds great - I'm definitely interested. I don't expect to have
> > >>> any major schedule conflicts in the next month, so this is a good  
> > >>> time.
> > >>>
> > >>> I wasn't able to commit the RUnit tests before embarking on a busy  
> > >>> July
> > >>> of traveling, so that's still on my plate. I also have some notes  
> > >>> on a
> > >>> few unresolved issues I've encountered while working with phylo4d
> > >>> objects, but I'll have to dust them off and remind myself of the  
> > >>> details
> > >>> before saying anything useful about that.
> > >>>
> > >>> Cheers,
> > >>> Jim
> > >>>
> > >>> Peter Cowan wrote:
> > >>>> phylobase devs,
> > >>>>
> > >>>> Last December, we had a very successful virtual hackathon.  However,
> > >>>> development has stalled since then.  Would folks be interested/ 
> > >>>> willing
> > >>>> to participate in a hackathon in the next month, focused on  
> > >>>> preparing
> > >>>> the package for a release to CRAN?  The school year is looming so I
> > >>>> suspect for many the sooner the better, though ESA is this week,  
> > >>>> which
> > >>>> will keep at least Steve occupied.
> > >>>>
> > >>>> * If you are able, what are the best days for you?
> > >>>>
> > >>>> * What needs to be done before we can submit the package to CRAN?   
> > >>>> How
> > >>>> long do you expect they will take?
> > >>>>
> > >>>>
> > >>>> Personally I'm free anytime.  I need to finish up some changes I've
> > >>>> started with the plotting functions, I suspect it will take me a day
> > >>>> or two wrap them up.
> > >>>>
> > >>>> 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
> > >> ____________________________________________
> > >> Marguerite A. Butler
> > >> Assistant Professor
> > >> Department of Zoology
> > >> University of Hawaii
> > >> 2538 McCarthy Mall, Snyder 405
> > >> Honolulu, HI  96822
> > >>
> > >> Dept: 808-956-8617
> > >> Lab:  808-956-5867
> > >> FAX:   808-956-9812
> > >> http://www.hawaii.edu/zoology/faculty/butler.html
> > >> http://www2.hawaii.edu/~mbutler
> > >> http://www.hawaii.edu/zoology/
> > >>
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> 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
> > 
> > 
> > _______________________________________________
> > 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