[Phylobase-devl] Rcpp and OS X compiliation

[Brian O'Meara]

Thank you all for your work on this.

Brian

On Jan 19, 2010, at 4:57 PM, Mark Holder wrote:

> Hi folks,
> 	Dirk, Romain Francois, Simon Urbanek, and I have had some more off- 
> thread email exchanges about this issue.  I think that it is now  
> resolved.
>
>
> Speaking for the phylo-informatics community, I'd like to sincerely  
> thank Dirk, Romain, and Simon for all of the help getting this  
> sorted out.
>
>
> The long term solution:
> 	Dirk and Romain are going to release Rcpp 0.7.3 soon. This version  
> will cause phylobase to statically link to libRcpp. No changes to  
> phylobase are required.
>
>
> The short term solutions. Either:
> 	1. install Rcpp and phylobase from source, or
> 	2. augment your dynamic library loading path (for example add $HOME/ 
> Library/R/2.10/library/Rcpp/lib/i386 to the list of directories in  
> the DYLD_LIBRARY_PATH environmental variable on Mac).
>
>
> Below I summarize the issues for those who are curious.
>
>
>
> all the best,
> Mark
>
>
>
>
> The gory details (as I understand them):
>
> 1. shared (or "dynamic") libraries contain a path to their  
> location.  I think that this field can also be just the name, but by  
> default it is the full path.  (On Mac, "otool -L libNAMEHERE.so"   
> lists this location. install_name_tool can be used to update this  
> info).
>
> 2. executables or other libraries that link to a dylib store the  
> path that the library lists for itself.  This info is used by the  
> loader at runtime to find all of the object code that the calling  
> code uses.
>
> 3. If the loader finds a library with the correct name in its  
> search, then it will load the library (even if the calling library  
> incorrectly lists its own location).  So the loading is robust to  
> moving the library, if you move it to a directory that is on the  
> search path (it still not a great idea to move your dynamic  
> libraries after linking to them).
>
> So, if phylobase was linked against libRcpp that was at /x/lib/ 
> libRcpp.dylib (and libRcpp lists its own location as "/x/lib/ 
> libRcpp.dylib") then when phylobase loads, it will be able to load  
> the functions supplied by libRcpp:	
> 	- if libRcpp is still at /x/lib/libRcpp.dylib, OR
> 	- if there is a library called libRcpp.dylib in the directories  
> that are always searched (eg. those libraries listed in  
> DYLD_LIBRARY_PATH, or those directories that R specifies to the  
> loader).
>
> 4. There is no binary package installation hook that would allow a  
> dynamic library to be modified when it is installed via the  
> install.packages mechanism.   So calling something like  
> install_name_tool as part of package installation so that each  
> library lists the correct (installed) location for itself is not an  
> option.
>
> Thus, when a binary form of phylobase was installed, it would refer  
> to a path to libRcpp.dylib that does not exist on the user's machine  
> (it will be a  a path on the build machine's filesystem).  So binary  
> installs of phylobase  were brittle.
>
> Furthermore, if one uses install.packages to install Rcpp, then the  
> library that you download will have the wrong path listed for its  
> own location.  If you then build phylobase against this version of  
> the library, the build and link will work but the loader will look  
> in the wrong place for the library (and the library(phylobase) call  
> will fail).
>
>
> The most robust solution seems to be static linking of Rcpp into  
> phylobase.  After a statically-linked version of pyhlobase.so is  
> created, then phylobase will no longer need to find libRcpp.*
>
>
>
> Building from source also works because then all of the libraries  
> list their own locations correctly.
>
>
>
>
>
>
>
>
>
>
> Mark Holder
>
> mtholder at ku.edu
> http://www.people.ku.edu/~mtholder/
>
> ==============================================
> Department of Ecology and Evolutionary Biology
> University of Kansas
> 6031 Haworth Hall
> 1200 Sunnyside Avenue
> Lawrence, Kansas 66045
>
> lab phone:  785.864.5789
>
> fax (shared): 785.864.5860
> ==============================================
>
>
>
>
>
>
>
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------------------------------------------------------
Brian O'Meara
http://www.brianomeara.info
Assistant Prof.
Dept. Ecology & Evolutionary Biology
U. of Tennessee, Knoxville

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