[Phylobase-devl] misc.
Brian O'Meara
bcomeara at nescent.org
Wed Dec 17 17:40:44 CET 2008
IRC channel is now up on freenode. Our channel is phylobase. Since
we're all in different timezones, I'm logging output to my computer
and posting it online every 5 minutes so we can see what went on
while we slept: you can see it at < http://snipurl.com/irclog>. Feel
free to add more sophisticated logging -- I don't know about IRC bots
and the like.
Brian
On Dec 16, 2008, at 11:32 PM, Steven Kembel wrote:
> Hi all,
>
> Noon eastern on Thursday works for me for a virtual meeting. Skype/
> Gizmo or whatever NESCent IT recommends is fine. How about an IRC
> channel as well for Thursday/Friday?
>
> Off the top of my head my preference is to work first on the bug and
> feature requests related to phylo4d objects and metadata, and then the
> tree traversal and ordering methods. This will initially involve going
> through the phylo4d constructors and methods and making sure
> everything is working well, or getting rid of methods that are broken,
> to allow submitting the package to CRAN.
>
> Hilmar mentioned implementing NeXML support in phylobase as a possible
> target. I think the feature request for metadata/annotation slot
> implementation for phylo4 and phylo4d objects should try to follow
> existing metadata/annotation standards as implemented in things like
> NeXML rather than coming up with another format, so I'd like to
> discuss this on Thursday as well.
>
> Cheers,
> Steve
>
> On Dec 16, 2008, at 2:29 PM, Brian O'Meara wrote:
>
>> Should we start on the back and forth regarding minihack planning and
>> agenda? Ben suggested noon Eastern for daily virtual meetings. Any
>> preferences on how to set them up, or should I just ask NESCent IT
>> for its current recommendation? How should we start adding things to
>> the agenda? We have 11 feature requests <https://r-forge.r-
>> project.org/tracker/?atid=491&group_id=111&func=browse> and 1 bug
>> <https://r-forge.r-project.org/tracker/?
>> atid=488&group_id=111&func=browse> on R-forge, but these haven't been
>> changed in months. We could add things there and modify their
>> priority and assignment, do it more informally over email, throw
>> things on a wiki, etc.
>>
>> Brian
>>
>> On Dec 8, 2008, at 3:15 PM, Ben Bolker wrote:
>>
>>> Yes.
>>>
>>> I was thinking of setting up another time for a preliminary
>>> skype/conference/chat meeting, but that feels like overkill.
>>> Perhaps we can set an agenda/tentative task assignments by
>>> back-and-forth over e-mail.
>>>
>>> cheers
>>> Ben
>>>
>>>
>>> Brian O'Meara wrote:
>>>> Hi, all. It appears that Dec. 18-19 are the only days when
>>>> everyone who
>>>> has filled out the poll can do the minihack (Thursday and Friday
>>>> of next
>>>> week). See the poll at <http://www.doodle.com/9pndm3xaszh7gpck>.
>>>> Shall
>>>> we thus schedule the minihack for both of those days?
>>>>
>>>> Brian
>>>>
>>>>
>>>> On Dec 5, 2008, at 7:44 PM, Marguerite Butler wrote:
>>>>
>>>>> Hi Folks,
>>>>>
>>>>> Sorry for the silence. Still teaching my two classes, so I'm
>>>>> pretty
>>>>> tied up.
>>>>>
>>>>> Basically next week (week of Dec. 15) and week of Jan 13 are the
>>>>> only
>>>>> possibilities for me. (I'll be spending some much needed time
>>>>> with my
>>>>> daughter over Xmas and then I have to get ready for the SICB
>>>>> meetings
>>>>> in the first week of Jan. (I'm back to work Jan 12, but things
>>>>> will be
>>>>> pretty nuts that day, so Jan 13 is the first day for me).
>>>>>
>>>>> Mike Alfaro and I are going to be teaching two sessions at SICB, a
>>>>> first day for complete beginners in R and a second evening
>>>>> session o
>>>>> comparative analysis in R, so if there is anything you'd like to
>>>>> show
>>>>> off, please let me know. Hopefully I can get stuff ready in
>>>>> time to
>>>>> get feedback from the developers:).
>>>>>
>>>>> Feel free to go ahead without me on the Hackathon, though, if my
>>>>> schedule is a problem.
>>>>>
>>>>> Marguerite
>>>>>
>>>>> On Dec 5, 2008, at 12:26 PM, Peter Cowan wrote:
>>>>>
>>>>>> The list was cc'd, and Steve has already filled out a slot in the
>>>>>> 'doodle'.
>>>>>>
>>>>>> peter
>>>>>>
>>>>>> On Dec 5, 2008, at 2:23 PM, Ben Bolker wrote:
>>>>>>
>>>>>>> For what it's worth, Thibaut sent his apologies --
>>>>>>> he's going to start a new postdoc very soon.
>>>>>>> (I don't remember if he cc'd this list.)
>>>>>>> Marguerite, Steve?
>>>>>>>
>>>>>>> Ben
>>>>>>>
>>>>>>> Peter Cowan wrote:
>>>>>>>> I've added my schedule to http://www.doodle.com/
>>>>>>>> 9pndm3xaszh7gpck
>>>>>>>>
>>>>>>>> On Dec 4, 2008, at 7:31 AM, Brian O'Meara wrote:
>>>>>>>>> On Dec 3, 2008, at 2:47 PM, Steven Kembel wrote:
>>>>>>>>>
>>>>>>>>>> Hi all,
>>>>>>>>>>
>>>>>>>>>>> * chat on the list about a deadline and milestones needed
>>>>>>>>>>> for a CRAN release? (My votes: merged plotting code, all
>>>>>>>>>>> known
>>>>>>>>>>> bugs fixed [I don't actually think that would be hard],
>>>>>>>>>>> node-
>>>>>>>>>>> labeling
>>>>>>>>>>> scheme updated).
>>>>>>>>>>> * have one or more additional conference calls?
>>>>>>>>>> Discussing this on the list or in a conference call would be
>>>>>>>>>> great. I
>>>>>>>>>> think we are in pretty good shape for most of these things.
>>>>>>>>>> -plotting code should be a straightforward merge of the
>>>>>>>>>> summer of
>>>>>>>>>> code
>>>>>>>>>> branch into trunk
>>>>>>>>
>>>>>>>> Agreed this shouldn't take long and might even happen before
>>>>>>>> the
>>>>>>>> virtual hackathon if I can find a few hours to button up loose
>>>>>>>> ends.
>>>>>>>>
>>>>>>>>>> I will go through the list of bugs/feature requests on R-
>>>>>>>>>> Forge and try to clean out the requests that have been dealt
>>>>>>>>>> with. If
>>>>>>>>>> others have fixed bugs/feature requests go ahead and change
>>>>>>>>>> their
>>>>>>>>>> status to resolved.
>>>>>>>>>> -The node-labeling scheme has been updated already unless
>>>>>>>>>> there
>>>>>>>>>> were
>>>>>>>>>> further changes needed.
>>>>>>>>>>
>>>>>>>>>>> * an ambitious plan: have a "virtual hackathon" sometime
>>>>>>>>>>> between now and mid-January, where we all agree to the best
>>>>>>>>>>> of our abilities to spend the same day or two investing
>>>>>>>>>>> a significant amount of hacking time ... we could have
>>>>>>>>>>> one or two 'plenary sessions' a day and do Skype/chat
>>>>>>>>>>> in between ... what do you think?
>>>>>>>>>> This sounds like a great idea, I'd be interested, will have
>>>>>>>>>> some
>>>>>>>>>> time
>>>>>>>>>> over the 'holidays' to work on this. What are people's
>>>>>>>>>> schedules
>>>>>>>>>> like
>>>>>>>>>> - would a brief call sometime in the next few weeks work?
>>>>>>>>> I'm generally unconstrained, as we're not traveling for the
>>>>>>>>> holidays.
>>>>>>>>> We can set up a poll to schedule a conference call once we
>>>>>>>>> have a
>>>>>>>>> general idea of when people can talk. I've started a poll
>>>>>>>>> about a
>>>>>>>>> mini-hackathon itself at http://www.doodle.com/
>>>>>>>>> 9pndm3xaszh7gpck .
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> 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
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>> 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
>>>>>
>>>>
>>>>
>>>> ________________________________
>>>> Brian O'Meara
>>>> NESCent
>>>> Durham, NC
>>>> http://www.brianomeara.info
>>>> ________________________________
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------------------
>>>> --
>>>> ---
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>>
>>> --
>>> 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
>>>
>>> _______________________________________________
>>> 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
>>
>>
>> ________________________________
>> Brian O'Meara
>> NESCent
>> Durham, NC
>> http://www.brianomeara.info
>> ________________________________
>>
>>
>>
>> _______________________________________________
>> 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
>
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________________________________
Brian O'Meara
NESCent
Durham, NC
http://www.brianomeara.info
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