[ADMB Users] [Developers] FW: myxomatosis example

Wed Oct 26 13:58:22 PDT 2011

Did this ever get resolved? I can't figure out how to use the contributed code any more.
I've tried
#include <contrib.h>	
#include <Users/molliebrooks/admb−trunk/contrib/statlib/dnbinom_eco.cpp>	

The second one used to work. The files are still in that location, but it doesn't work. How should I do this?

thanks,
Mollie

On 3 Aug 2011, at 12:43 AM, bigA wrote:

> Just out of curiosity, why not have a second package for user contributed code? Then as individual users want to extend their personal library of admb functions they would already have a standardized build process with a make file already started to build from.   It could also help establish some coding conventions,  across different user's contributed code, and a coherent way for users to include documentation  with the functions they submit. Finally it could also be useful to ensure that credit is given to those who contribute; admb is an open source project and it is nice make sure that people's names are on their work.  I would be willing to help with this, but I want to know how the admb establishment feels.
> Aaron
> 
> On Tue, Aug 2, 2011 at 7:58 PM, Steve Martell <s.martell at fisheries.ubc.ca> wrote:
> I think Johnoel's idea of a contrib.lib and contrib.h would work best, and the end user would still have to have put #include <contrib.h> in the GLOBALS_SECTION.  I'm hesitant to modify the existing makefiles to have the buildbot include the contributed code in the builds, so I did not do this.  It should be possible, however, to create a makefile in the contrib directory that would build the contrib.lib and put this in the lib directory of the build.  Makefiles are pretty new to me so I'd need some help on this one.
> 
> Steve
> On 2011-08-02, at 2:02 PM, Johnoel Ancheta wrote:
> 
> > I may have a easy solution, but will need to test.  It involves creating a contrib.lib and contrib.h that
> > gets built with admb.  Easier for the end user...
> >
> > On 8/2/11 10:48 AM, Mark Maunder wrote:
> >> John,
> >>
> >> I thought that the idea was to have the contributed code compiled in the libraries, but not include the #include statement somewhere so that the user had to physically put the include statement in their tpl (similar to how an R user has to physically load the library). The messy part is having to use the whole path to the code and not just the name of the library
> >>
> >> Mark
> >>
> >> -----Original Message-----
> >> From: developers-bounces at admb-project.org [mailto:developers-bounces at admb-project.org] On Behalf Of John Sibert
> >> Sent: Tuesday, August 02, 2011 1:41 PM
> >> To: developers at admb-project.org
> >> Subject: Re: [Developers] FW: myxomatosis example
> >>
> >> Well including stuff in the GLOBALS_SECTION does not seem particularly messy, Dave is correct the usual way is with a header file and a library.
> >>
> >> The practical question is how are the libraries assembled? Each OS/architecture/compiler combination brings unique problems. That is why we have the buildbot for the ADMB code. It might be feasible to include the contributed contribted code, but in my opinion the ADMB Project should not be responsible for maintenance of user-contributed code.
> >> Could we ask code contributors to create an appropriate header file and a makefile to create a library for their code? If so then users of the contributed code would have the option of either including the source code in the tpl or customizing the makefile to build libraries appropriate to their system.
> >>
> >> John
> >>
> >> On 08/01/2011 02:08 PM, dave fournier wrote:
> >>> On 11-08-01 04:15 PM, Mark Maunder wrote:
> >>>
> >>> The usual way is to include a header file and then to link in a
> >>> library with the compiled code.
> >>>
> >>>> Can anyone give advice on how to include user contributed libraries
> >>>> in the Globals section. This looks too messy. Can't you just do
> >>>> "#include ecolib"
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Mark
> >>>>
> >>>> *From:*Mollie Brooks [mailto:mbrooks at ufl.edu]
> >>>> *Sent:* Monday, August 01, 2011 4:03 PM
> >>>> *To:* Mark Maunder
> >>>> *Subject:* myxomatosis example
> >>>>
> >>>> Hi Mark,
> >>>>
> >>>> I did an example from Ben's book. I'm also working on another one.
> >>>> This one requires a vectorized version of the dgamma function which I
> >>>> just added to Steve's statlib on the svn. I'd like any suggestions
> >>>> you might have, especially on the globals section. I think the
> >>>> developers should have a talk about making it as easy as possible for
> >>>> users to include libraries from the contrib directory. Maybe these
> >>>> should get moved to the include directory automatically when we
> >>>> compile. Also, the library pow_vectorized_RE should probably be
> >>>> incorporated into the core source.
> >>>>
> >>>> I did it using R2admb which currently doesn't work for windows, but
> >>>> I'm hoping Ben will have it working later this month.
> >>>>
> >>>> cheers,
> >>>>
> >>>> Mollie
> >>>>
> >>>>
> >>>> _______________________________________________
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> >>>
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> >> --
> >> John Sibert
> >> Emeritus Researcher, SOEST
> >> University of Hawaii at Manoa
> >>
> >> Visit the ADMB project http://admb-project.org/
> >>
> >>
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