[Phylobase-devl] Rcpp and OS X compiliation

Peter Cowan pdc at berkeley.edu
Wed Dec 16 19:16:13 CET 2009

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.

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'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.


> Dirk
> -- 
> Three out of two people have difficulties with fractions.
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