[Rcpp-devel] Building shared libs with Rcpp does not work as before after Debian update ( function 'dataptr' not provided by package 'Rcpp' )

Wed Mar 19 13:32:39 CET 2014

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 at 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
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