[Rcpp-devel] Symbol not found when including an external library

[Simon Zehnder]

The error was on my system. After trying several things (many thanks to Steve Jaffe at this point, who gave not up on me :)) I decided to make a reinstall of my system. I reinstalled the compiler and build R with gcc 4.8.1. I was then able to successfully install my package with the suggested configuration below. 

Thanks to all for helping me out here.

Best

Simon

On Sep 4, 2013, at 7:30 PM, Dirk Eddelbuettel <edd at debian.org> wrote:

> 
> On 4 September 2013 at 18:51, Simon Zehnder wrote:
> | Dear Rcpp::Users, Rcpp::Devels,
> | 
> | I am following the ongoing discussion 'How to use external C++ libraries in R packages withRcpp' (Makevars are still one of my weaknesses) and I have a related question. 
> | 
> | I am trying to use the C++ optimization library nlopt (http://ab-initio.mit.edu/wiki/index.php/NLopt) in my package that is based on RcppArmadillo. In a first step I installed nlopt in a subfolder of the 'src' folder of my package structure (so I have '/src/nlopt-2.3'). Second, I included the header file into my source file right below '#include <RcppArmadillo.h>'. Then I set my Makevars file to:
> | 
> | ## Use the R_HOME indirection to support installations of multiple R version
> | NLOPT_VERSION = 2.3
> | 
> | NLOPT_LIBS = -lm nlopt-${NLOPT_VERSION}/lib/libnlopt_cxx.a
> | 
> | NLOPT_INCL = -I./nlopt-${NLOPT_VERSION}/include
> | 
> | PKG_CPPFLAGS = ${NLOPT_INCL}
> | PKG_CFLAGS = -pipe ${NLOPT_INCL}
> | PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` ${NLOPT_LIBS}
> | 
> | Calling 'R CMD INSTALL packageName' compiles without errors but produces the well-known error during loading the shared library:
> | 
> | Error in dyn.load(file, DLLpath = DLLpath, ...) :
> |   unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/finmix/libs/finmix.so':
> |   dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/finmix/libs/finmix.so, 6): Symbol not found: __ZNSt8__detail15_List_node_base11_M_transferEPS0_S1_
> 
> Briefly:
> 
> i)   Please show the actual linking step.
> 
> ii)  Mixing shared and static is a bit messy, but I have done it too I
>      think. You may want to try _an absolute path_ to the .a library,
>      and a different link position, eg place ${NLOPT_LIBS} first.
> 
> This is definitely doable.
> 
> Dirk
> 
> 
> | I find the missing symbol (using 'nm -A libnlopt_cxx.a | grep "transfer"' on the shell) in the static library of nlopt (libnlopt_cxx.a) to which I link in the Makevars, but I do not know yet, how I have to modify the Makevars to include also the static library of nlopt into the shared library of my package. Does anyone have a suggestion how to do it? 
> | 
> | 
> | Best
> | 
> | Simon
> | 
> | 
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> 
> -- 
> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com