[Phylobase-devl] Rcpp and OS X compiliation

[Brian O'Meara]

On Dec 16, 2009, at 2:15 PM, Dirk Eddelbuettel wrote:

>
> On 16 December 2009 at 10:16, Peter Cowan wrote:
> | On Dec 16, 2009, at 7:06 AM, Dirk Eddelbuettel wrote:
> |
> | >
> | > On 16 December 2009 at 09:19, Hilmar Lapp wrote:
> | > | On Dec 16, 2009, at 7:36 AM, Dirk Eddelbuettel wrote:
> | > |
> | > | > What I don't understand is why the lib that R loads itself  
> (in the
> | > | > Rcpp/libs/
> | > | > directory) is a .so.  Is that how it is supposed to be OS X?
> | > |
> | > |
> | > | No, it's the .dylib that it's supposed to be loading.
> | >
> | > Ok, maybe Hilmar, Brian and I should take this off-list then.   
> My best idea
> | > (being the OS X ignoramus that I am) were to look at two other  
> (and small !!)
> | > package that also link against Rcpp:
> | >
> | > -- Earth Mover Distance
> | >    https://r-forge.r-project.org/projects/earthmovdist/
> | >    No log at R-Forge because no recent changes
> | >
> | > -- RInside
> | >    https://r-forge.r-project.org/projects/rinside/
> | >    No log at R-Forge because I had a stupid mistake in a change
> | >    on Sunday that I fixed yesterday -- will work now but hasn't  
> been
> | >    rebuilt on R-Forge yet
> | >
> | > We simply need a smaller working example, see the exact gcc  
> invocation on OS
> | > X and then compare what the more complicated (as ncl enters etc)  
> phylobase
> | > does.  This ain't brain surgery and we will get this fixed.
> |
> | I don't mind if this stays on list.  Many of us are OS X users,  
> but don't understand the build process very well.
>
> Ok. I keep railing then :) I understand the build process [ and  
> there is only
> one lesson: let R do as much as possible and don;t get in the way;  
> Simon
> Urbanek drilled that into my head with some success ... ] but am  
> clueless
> with OS X.
>
> | I've had similar problems in the past, and attributed it to NCL  
> not being
> | build using the R make variables.  This is what I *thought* was  
> going on,
> | it might be completely off base.  From 10.5 to 10.6 Apple changed  
> the
> | default build architecture from i386 to x86_64.  R has typically  
> been
> | distributed as a 32 bit (i386) build.  So all was fine when NCL was
> | building as the default in 10.5, but when moving to 10.6 32 bit R  
> and the
> | default build doesn't work.  So I use the 64bit build of R to  
> install and
> | run phylobase and it works fine.  But, doesn't constitute a general
> | solution.
>
> I got to this via the automated generation of binary CRAN package  
> in .deb
> form which I do at http://debian.cran.r-project.org.  phylobase failed
> miserably, and I blame ncl.  The configure files are old and should  
> get
> replaced.  For Linux, I essentially sidestepped ncl's configure and  
> used
> Makefile.win with one modification. Then it worked. That would not  
> work for
> OS X due to multiarch.  But we will get to that.
>
> That said, we currently have an issue with a part I am maintaining  
> (Rcpp) and
> I would like that squared off first.
>
> Hence my request (see above in the quoted part) for an OS X  
> volunteer to
> look with me off-line at success / failure of RInside or EarthMovDist.

I would be able to do this after Jan 9 (trying to get a grant in by  
NSF's deadline), but someone else should feel free to jump in.

Thanks, all.

Brian


>
> | I'm sure the make files for NCL could be greatly simplified which  
> could
> | help. But, it is currently beyond my abilities, and I don't  
> currently have
> | the time to learn the make.
>
> Ideally we would able to assume that the user has already installed  
> ncl. In
> the real world down here that may never be the case, alas.
>
> Dirk
>
> -- 
> Three out of two people have difficulties with fractions.

------------------------------------------------------
Brian O'Meara
http://www.brianomeara.info
Assistant Prof.
Dept. Ecology & Evolutionary Biology
U. of Tennessee, Knoxville