Hi, I found the problem. The solution is as always: simple and stupid, and difficult to find. When using my shared library, I used to do this: >dyn.load("test.so") >.Call("test", x_ = 2, y_ = 3) And got the error: function 'dataptr' not provided by package 'Rcpp'
I did not load the Rcpp library for that, because all the Rcpp routines were already linked into my test.so! The solution now is to do >require("Rcpp") before. And everything works! Maybe it is equally simple to include the boost libraries into R, to improve the portability of my final package ... All the best, Andreas On 18.03.2014 15:45, Andreas Recke wrote: > Hi, > > maybe I can add some more details about my problem. It has been > addressed before at stackoverflow: > > http://stackoverflow.com/questions/21657575/what-does-this-mean-in-lme4-function-dataptr-not-provided-by-package-rcpp > > with the question: > "I'm trying to do LMM using lme4, and this message pops up: > > Error in initializePtr() : function 'dataptr' not provided by package 'Rcpp' > > What should I do?" > > As proposed there in the responses, I reinstalled Rcpp, RcppArmadillo > and RcppEigen (in this order) from source packages. > However, when I look with nm into RcppEigen.so in the library folder, I > find the following: > > andreas@persephone:~/R/x86_64-pc-linux-gnu-library/3.0/RcppEigen/libs$ > nm RcppEigen.so | grep " u " > > > > > 0000000000238e70 u _ZGVZ13error_occuredvE3fun > 0000000000238e80 u _ZGVZ19reset_current_errorvE3fun > 0000000000238bb8 u _ZGVZ20rcpp_get_stack_tracevE3fun > 0000000000238bb0 u _ZGVZ20rcpp_set_stack_traceP7SEXPRECE3fun > 0000000000238e60 u _ZGVZ22rcpp_get_current_errorvE3fun > 0000000000238ba0 u _ZGVZ7dataptrP7SEXPRECE3fun > 0000000000238ba8 u _ZGVZ8demangleRKSsE3fun > 0000000000238e90 u _ZGVZN4Rcpp8internal18get_Rcpp_namespaceEvE3fun > 0000000000238e10 u _ZZ13error_occuredvE3fun > 0000000000238e30 u _ZZ19reset_current_errorvE3fun > 0000000000238b80 u _ZZ20rcpp_get_stack_tracevE3fun > 0000000000238b70 u _ZZ20rcpp_set_stack_traceP7SEXPRECE3fun > 0000000000238e00 u _ZZ22rcpp_get_current_errorvE3fun > 0000000000238b60 u _ZZ7dataptrP7SEXPRECE3fun <----- > here is the missing function > 0000000000238b90 u _ZZ8demangleRKSsE3fun > 0000000000238e20 u _ZZN4Rcpp8internal18get_Rcpp_namespaceEvE3fun > 0000000000238e40 u > _ZZN5Eigen8internal20manage_caching_sizesENS_6ActionEPlS2_E13m_l1CacheSize > 0000000000238e50 u > _ZZN5Eigen8internal20manage_caching_sizesENS_6ActionEPlS2_E13m_l2CacheSize > 0000000000033708 u > _ZZN5Eigen8internal23triangular_solve_vectorIddlLi1ELi1ELb0ELi0EE3runElPKdlPdE10PanelWidth > 0000000000033718 u > _ZZN5Eigen8internal23triangular_solve_vectorIddlLi1ELi2ELb0ELi0EE3runElPKdlPdE10PanelWidth > 0000000000033700 u > _ZZN5Eigen8internal23triangular_solve_vectorIddlLi1ELi2ELb0ELi1EE3runElPKdlPdE10PanelWidth > 00000000000336f8 u > _ZZN5Eigen8internal23triangular_solve_vectorIddlLi1ELi5ELb0ELi0EE3runElPKdlPdE10PanelWidth > 00000000000336f0 u > _ZZN5Eigen8internal23triangular_solve_vectorIddlLi1ELi6ELb0ELi1EE3runElPKdlPdE10PanelWidth > 0000000000033710 u > _ZZN5Eigen8internal32triangular_matrix_vector_productIlLi2EdLb0EdLb0ELi0ELi0EE3runEllPKdlS4_lPdlRS3_E10PanelWidth > > > This completely fits the above quoted error message. But I don't know > how to solve this. Can you help? > > Best regards, > Andreas > > > > > > > > On 18.03.2014 11:43, Andreas Recke wrote: >> Hi, >> >> until recently, I used a very simple mechanism to compile and link my >> C++/Rcpp/RcppArmadillo code for using it in R. >> Since the last update, however, something has changed with the linking, >> and the Rcpp shared library is not linked to >> the final libary as before. >> My question is, whether I need to change the my code to take these >> changes into account? Is there a compatibility problem >> with earlier versions of R and Rcpp? >> I would like to have at least the option to use the command line to >> compile my code and to have it working even with different >> versions of R and Rcpp, especially because I found a way to use the >> THRUST library for parallel computing with Rcpp, Boost and R. >> >> So here is my problem: >> >> ******************* test.cpp *************** >> #include <iostream> >> #include <iomanip> >> #include <cmath> >> #include <RcppArmadillo.h> >> >> using namespace Rcpp; >> >> double norm(double x, double y) >> { >> return sqrt(x*x + y*y); >> } >> >> RcppExport SEXP norm_wrapper(SEXP x_,SEXP y_) >> { >> // step 0: convert input to C++ types >> double x = as<double>(x_), y= as<double>(y_); >> // step 1: call the underlying C ++ function >> double res = norm (x,y); >> // step 2: return the result as a SEXP >> return wrap(res); >> } >> ******************* >> >> *************** my makevars **************** >> >> PKG_CXXFLAGS=$(shell Rscript -e "Rcpp:::CxxFlags()") $(shell Rscript -e >> "RcppArmadillo:::CxxFlags()") >> PKG_LIBS=$(shell Rscript -e "Rcpp:::LdFlags()") $(LAPACK_LIBS) $(BLAS_LIBS) >> $(FLIBS) -lboost_system -lboost_thread >> >> ******************************************** >> >> >> ************* in bash, I compile with *********** >> R CMD SHLIB test.cpp >> >> **************************************************** >> >> ************* in R console **************** >> >>> dyn.load("test.so") >>> .Call("norm_wrapper", x_=2, y_=3) >> and I get the error message, that function "dataptr" is not provided by >> package "Rcpp" ... >> >> ****************************************** >> looking at test.so with nm , function "dataptr" is marked as unknown >> >> Until recently, the above described procedure worked fine. Maybe it is >> possible to keep it available for >> compatibility reasons. >> >> Andreas >> >> >> By the way: I have R version 3.0.3 (2014-03-06) -- "Warm Puppy" on >> x86_64-pc-linux-gnu (64-bit), with Rcpp 0.11.1 from 3/12/2014 >> -- Dr. Andreas Recke Facharzt Klinik für Dermatologie, Allergologie und Venerologie Universitätsklinikum Schleswig-Holstein, Campus Lübeck Ratzeburger Allee 160 23538 Lübeck Tel.: +49 451 500 2530 Fax.: +49 451 500 2981 [http://www.uksh.de/skin/uksh/tpl/infoportal/img/uk-sh_logo.gif] Universitätsklinikum Schleswig-Holstein Rechtsfähige Anstalt des öffentlichen Rechts der Christian-Albrechts-Universität zu Kiel und der Universität zu Lübeck Vorstandsmitglieder: Prof. Dr. Jens Scholz (Vorsitzender), Peter Pansegrau, Christa Meyer Vorsitzender des Aufsichtsrates: Rolf Fischer Bankverbindungen: Förde Sparkasse BLZ 210 501 70 Kto.-Nr. 100 206, IBAN: DE14 2105 0170 0000 1002 06 SWIFT/BIC: NOLA DE 21 KIE Commerzbank AG BLZ 230 800 40 Kto.-Nr. 300 041 200, IBAN: DE17 2308 0040 0300 0412 00 SWIFT/BIC: DRES DE FF 230 Diese E-Mail enthält vertrauliche Informationen und ist nur für die Personen bestimmt, an welche sie gerichtet ist. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, bitten wir Sie, uns hiervon unverzüglich zu unterrichten und die E-Mail zu vernichten. Wir weisen darauf hin, dass der Gebrauch und die Weiterleitung einer nicht bestimmungsgemäß empfangenen E-Mail und ihres Inhalts gesetzlich verboten sind und ggf. Schadensersatzansprüche auslösen können. _______________________________________________ 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