[Phylobase-devl] Rcpp and OS X compiliation

Brian O'Meara omeara.brian at gmail.com
Tue Dec 15 21:26:13 CET 2009

Hi, all. Dirk Eddelbuettel [1] has been working to pull Rcpp [2]  
source code out from phylobase and make it a dependency instead. Rcpp  
is used to interact with C++ code -- we included its source in  
phylobase because we used it to interact with NCL but at the time Rcpp  
was abandoned and not available in many CPAN mirrors, but it has since  
been taken over by Dirk. His phylobase changes are committed to R- 
forge trunk, but there are errors on the Mac build (see command check  
[3]). Dirk's been debugging it (with me trying to help by typing what  
I'm told to on my mac) but we're still running into problems. Anyone  
else want to take a crack at it?

Things to know:
Rcpp Template will throw an error if you install from source. This is  
known, and apparently not relevant to our problem.
I'm getting errors like "i686-apple-darwin9-g++-4.2.1: PKG_LIBS=/ 
libRcpp.a: No such file or directory" when doing

R CMD SHLIB PKG_CXXFLAGS="-I/Library/Frameworks/R.framework/Resources/ 
library/Rcpp/lib/i386 -Incl/ncl" PKG_LIBS="/Library/Frameworks/ 
R.framework/Resources/library/Rcpp/lib/i386/libRcpp.a -Lncl/ncl/.libs - 
lncl" -o phylobase.dylib *cpp *c

even though /Library/Frameworks/R.framework/Resources/library/Rcpp/lib/ 
i386/libRcpp.a clearly exists on my system:

ls -ulth /Library/Frameworks/R.framework/Resources/library/Rcpp/lib/ 
-rw-r--r--  1 bomeara  admin   1.1M Dec 15 14:13 /Library/Frameworks/ 

I'd suspect something off with just my system, other than the fact  
that R-forge is also having issues.


[1]: http://dirk.eddelbuettel.com/
[2]: http://dirk.eddelbuettel.com/code/rcpp.html
[3]: http://r-forge.r-project.org/R/?group_id=111&log=check_x86_64_mac&pkg=phylobase&flavor=patched

Brian O'Meara
Assistant Prof.
Dept. Ecology & Evolutionary Biology
U. of Tennessee, Knoxville

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