[Phylobase-devl] Rcpp and OS X compiliation

[Ben Bolker]

Mark Holder wrote:
> Hi folks,
> 	Thanks to Brian for helping me get up and running on this.
> 
> Here is what I'm seeing on Mac 10.5.8 with R 2.10.1.
> 
> I ran
> #############################
> $ R
>  > install.packages(c("ape", "Rcpp"))
> Warning in install.packages(c("ape", "Rcpp")) :
>     argument 'lib' is missing: using '/Users/mholder/Library/R/2.10/ 
> library'
> ....
> #############################
> despite the warning it ran (I'm not R-savvy enough to know if this  
> indicates a problem).

  No.  It's putting the package in a default location (why it issues a
warning in this case is another conversation).

> I was able to call library(Rcpp) and library(ape) from within R with  
> no errors.
> 
> 
> I then ran:
> ########################
> $ svn checkout svn://svn.r-forge.r-project.org/svnroot/phylobase
> ...
> $ cd phylobase
> $ R CMD INSTALL pkg
> * installing to library ‘/Users/mholder/Library/R/2.10/library’
> * installing *source* package ‘phylobase’ ...
> ...
> ########################
> There was lots of configure and make output, of course.
> Of note to me were the
> 
> 	-L/Users/mholder/Library/R/2.10/library/Rcpp/lib/i386 -lRcpp flags in  
> the linking step command.
> 
> 
> I did get a ld warning: duplicate dylib /usr/local/lib/libgcc_s.1.dylib
> 
> but the build exited without error.
> 
> When I try to import phylobase I get an error similar to the one seen  
> on https://r-forge.r-project.org/R/?group_id=111&log=check_x86_64_mac&pkg=phylobase&flavor=patched
> 
> Specifically I see:
> 
> 
[snip]


> library(phylobase)
> Loading required package: grid
> Loading required package: ape
> Loading required package: Rcpp
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>    unable to load shared library '/Users/mholder/Library/R/2.10/ 
> library/phylobase/libs/i386/phylobase.so':
>    dlopen(/Users/mholder/Library/R/2.10/library/phylobase/libs/i386/ 
> phylobase.so, 6): Library not loaded: /Builds/Rdev-web/QA/Simon/ 
> packages/tiger-universal/Rlib/2.10/Rcpp/lib/i386/libRcpp.dylib
>    Referenced from: /Users/mholder/Library/R/2.10/library/phylobase/ 
> libs/i386/phylobase.so
>    Reason: image not found
> Error: package/namespace load failed for 'phylobase'
> 
> #################################################################################
> 
> 
> But if I alter my shell's env to contain the path to libRcpp.dylib  
> then it works:
> 
> #################################################################################
> $ ls /Users/mholder/Library/R/2.10/library/Rcpp/lib/i386/
> Rcpp                   RcppCommon.h           RcppDateVector.h        
> RcppDatetimeVector.h   RcppFunction.h         RcppMatrix.h            
> RcppNumList.h          RcppResultSet.h        RcppStringVector.h      
> RcppVector.h           libRcpp.a
> Rcpp.h                 RcppDate.h             RcppDatetime.h          
> RcppFrame.h            RcppList.h             RcppMatrixView.h        
> RcppParams.h           RcppSexp.h             RcppStringVectorView.h  
> RcppVectorView.h       libRcpp.dylib
> $ export DYLD_LIBRARY_PATH=/Users/mholder/Library/R/2.10/library/Rcpp/ 
> lib/i386
> $ r
> 
[snip successful attempt]
> 
> So it appears to be an issue of the dynamic linker not finding the  
> right version of libRcpp.dylib
> 
> 
> I'm not sure how to fix it other than altering the user's env (which  
> is obviously not ideal).  

  No, but it might be an interim hack: R has Sys.getenv() and
Sys.setenv() which might be usable ?  (although they might have to be
called too early in the package-loading process)

> Are there other Rcpp libraries that I could  
> try out to see if they have similar problems on my machine?

http://cran.r-project.org/web/packages/Rcpp/index.html  says

	Reverse depends: 	RInside, RQuantLib

 so you could try those ...

  cheers
   Ben

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