[Phylobase-devl] Rcpp and OS X compiliation

Dirk Eddelbuettel edd at debian.org
Wed Dec 16 20:15:18 CET 2009

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'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.


Three out of two people have difficulties with fractions.

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