[Rcpp-devel] Building shared libs with Rcpp does not work as before after Debian update

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

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

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