Thanks for your explanation, Dirk! Indeed, I looked at Armadillo documentation, but it was not clear what was the kind of return.
Regarding the linking error, I had created the package using Rcpp.package.skeleton (because I didn't know I was going to use RcppArmadillo), and then I made the necessary changes according to documentation ( http://romainfrancois.blog.free.fr/index.php?post/2010/05/19/RcppArmadillo-0.2.1). So I created the package again using "RcppArmadillo.package.skeleton" and everything worked fine! Actually, what "RcppArmadillo.package.skeleton" creates is slightly different from what is described on documentation (maybe it is system dependent): - Documentation # Makevars PKG_LIBS = $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()" ) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) # Makevars.win PKG_LIBS = $(shell Rscript.exe -e "Rcpp:::LdFlags()") $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) - Documentation # Makevars PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) # Makevars.win PKG_LIBS = $(shell $(R_HOME)/bin/Rscript.exe -e "Rcpp:::LdFlags()") $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) So, it seems that the R libraries was not being imported during the package compilation; problem solved! Regards, João Daniel 2013/3/11 Dirk Eddelbuettel <e...@debian.org> > > > On 11 March 2013 at 22:42, João Daniel Nunes Duarte wrote: > | Hello, > | > | I'm trying to calculate principal component using 'princomp' function > from > | RcppArmadillo. Here's the cpp code: > | > | #include <RcppArmadillo.h> > | > | RcppExport SEXP pca(SEXP mats) { > | try { > | > | Rcpp::NumericMatrix matr(mats); > | int n = matr.nrow(), k = matr.ncol(); > | > | arma::mat mat(matr.begin(), n, k, false); > | arma::colvec pca; > | > | pca = arma::princomp(mat); > | > | return Rcpp::wrap(mat); > | > | } catch(...) { > | ::Rf_error("c++ error"); > | } > | } > | > | However, when I "R CMD check" the package, I get the following error: > | > | ** testing if installed package can be loaded > | Error in dyn.load(file, DLLpath = DLLpath, ...) : > | unable to load shared object > '/home/tecto/cpp/Rcpp/amora.Rcheck/amora/libs/ > | amora.so': > | /home/tecto/cpp/Rcpp/amora.Rcheck/amora/libs/amora.so: undefined > symbol: > | dgesvd_ > | Error: loading failed > | Execution halted > | > | I've read the Armadillo documentation for that function (http:// > | arma.sourceforge.net/docs.html#princomp), however it was not clear to > me how to > | use it correctly. > | > | Does my code have any mistake? > > Yes, several in fact. princomp() returns a matrix, not a vector. You were > trying to return mat when you probably meant to return pca. > > As for your linking error: should not happen. On all systems, > RcppArmadillo > should get these BLAS functions from R by linking to R. Unless your R is > built in a weird way. > > Here is what I get in the slightly corrected (and rewritten to use > sourceCpp() instead) example below: > > > R> sourceCpp("/tmp/joao.cpp") > > R> M <- matrix(1:9, 3, 3) > > R> localpca(M) > 1.0000 4.0000 7.0000 > 2.0000 5.0000 8.0000 > 3.0000 6.0000 9.0000 > > 0.5774 0.8165 0 > 0.5774 -0.4082 -0.7071 > 0.5774 -0.4082 0.7071 > > [,1] [,2] [,3] > [1,] 0.57735 0.816497 0.000000 > [2,] 0.57735 -0.408248 -0.707107 > [3,] 0.57735 -0.408248 0.707107 > R> > > > The program follows: > > > ----------------------------------------------------------------------------- > > #include <RcppArmadillo.h> > > // [[Rcpp::depends(RcppArmadillo)]] > > // [[Rcpp::export]] > Rcpp::NumericMatrix localpca(Rcpp::NumericMatrix matr) { > int n = matr.nrow(), k = matr.ncol(); > arma::mat mat(matr.begin(), n, k, false); > Rcpp::Rcout << mat << std::endl; > arma::mat pca = arma::princomp(mat); > Rcpp::Rcout << pca << std::endl; > return Rcpp::wrap(pca); > } > > /*** R > M <- matrix(1:9, 3, 3) > localpca(M) > */ > > > ----------------------------------------------------------------------------- > > And for what it is worth, R returns the same (modulo ordering): > > R> prcomp(M) > Standard deviations: > [1] 1.73205 0.00000 0.00000 > > Rotation: > PC1 PC2 PC3 > [1,] 0.57735 0.000000 0.816497 > [2,] 0.57735 -0.707107 -0.408248 > [3,] 0.57735 0.707107 -0.408248 > > > > Hth, Dirk > > | > | Cheers, > | > | João Daniel > | > | ---------------------------------------------------------------------- > | _______________________________________________ > | Rcpp-devel mailing list > | Rcpp-devel@lists.r-forge.r-project.org > | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel > -- > Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com >
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