[Rcpp-devel] RcppArmadillo solve function, dyn.load error

[Ayn Leslie-Cook]

Dirk,

thank you kindly - that works just as you say.

And also, thank you for all of the answers to Rcpp questions on
stackoverflow and elsewhere - they've been immensely helpful throughout
this project. Just about every time I have a question, you've already
answered it.   :)

Many thanks,

ayn





On Sun, May 6, 2012 at 3:29 PM, Dirk Eddelbuettel <edd at debian.org> wrote:

>
> Ayn,
>
> On 6 May 2012 at 14:38, Ayn Leslie-Cook wrote:
> | Hi all,
> |
> | I'm a student at the University of Washington and my course project this
> spring
> | involves rewriting the 'svmpath' R package into C++ using Rcpp and
> | RccpArmadillo.  Everything runs beautifully until I try to include the
> | function below:
> |
> | vec solveKstar(mat Kstar){
> |   vec onestar = ones<vec>(Kstar.n_cols);
> |   onestar[0]=0;
> |
>
> |   vec solution;
> |
>
> |   solution=solve(trimatu(Kstar),onestar);
> |   return solution;
> | }
> |
> | If I run R CMD INSTALL on my package removing the call to 'solve'
> everything
> | runs fine, but if I included the call to 'solve' then the R CMD INSTALL
> input
> | is
> |
> |
> | // all the typical output
> |
> | * installing to library ‘/net/home/aynlc3/Rlib’
> | * installing *source* package ‘aynSVMpath’ ...
> | ** libs
> | g++ -I/usr/share/R/include -DNDEBUG
> -I"/net/home/aynlc3/Rlib/Rcpp/include"
> | -I"/net/home/aynlc3/Rlib/RcppArmadillo/include"   -fpic  -O3 -pipe  -g
> -c
> | aynSVMpath.cpp -o aynSVMpath.o
> | g++ -I/usr/share/R/include -DNDEBUG
> -I"/net/home/aynlc3/Rlib/Rcpp/include"
> | -I"/net/home/aynlc3/Rlib/RcppArmadillo/include"   -fpic  -O3 -pipe  -g
> -c
> | svmHelpers.cpp -o svmHelpers.o
> | g++ -shared -o aynSVMpath.so aynSVMpath.o initializations.o svmHelpers.o
> | usetFunctions.o -L/net/home/aynlc3/Rlib/Rcpp/lib -lRcpp
> -Wl,-rpath,/net/home/
> | aynlc3/Rlib/Rcpp/lib -L/usr/lib/R/lib -lR
> | installing to /net/home/aynlc3/Rlib/aynSVMpath/libs
>
> Your src/Makevars is insufficient -- use something like
>
>  PKG_LIBS= `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS)
> $(BLAS_LIBS) $(FLIBS)
>
> so that you link against LAPACK and BLAS as well.
>
> | ** R
> | ** preparing package for lazy loading
> | ** help
> | *** installing help indices
> | ** building package indices
> | ** testing if installed package can be loaded
> |
> |            // then
> |
> | Error in dyn.load(file, DLLpath = DLLpath, ...) :
> |   unable to load shared object '/net/home/aynlc3/Rlib/aynSVMpath/libs/
> | aynSVMpath.so':
> |   /net/home/aynlc3/Rlib/aynSVMpath/libs/aynSVMpath.so: undefined symbol:
> | dtrtrs_
> |
> |
> | If I change 3rd and 4th lines of the 'solveKstar' function to:
> |
> |   vec solution;
> |
>
> |
> |   solution=solve(Kstar,onestar);    // removing the call to 'trimatu'
> |
> | the R CMD INSTALL output has the same typical output above, but with the
> | following change to the error
> |
> | Error in dyn.load(file, DLLpath = DLLpath, ...) :
> |   unable to load shared object '/net/home/aynlc3/Rlib/aynSVMpath/libs/
> | aynSVMpath.so':
> |   /net/home/aynlc3/Rlib/aynSVMpath/libs/aynSVMpath.so: undefined symbol:
> | dgels_
> |
> |
> | The symbols 'dtrtrs_' and 'dgels_' are not part of my code;  from digging
> | online, I believe these are coming from the lapack library, but I'm not
> sure
> | how to proceed with that knowledge.  Does anyone have any advice?
>
> Yes, once you link with LAPACK and BLAS you should be fine.  Let us know if
> that works.
>
> Dirk
>
> |  Also, if relevant, I'm running R 2.15.0, Rcpp_0.9.10 and
> | RcppArmadillo_0.3.0.2 on mosix.
> |
> | Many thanks,
> |
> | Ayn
> |
> |
> |
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