[Rcpp-devel] Package compilation error after a Mac update (related to the use of module and .constructor<const Rcpp::NumericVector &, int>()

Robin GIRARD robin.girard at mines-paristech.fr
Mon May 6 11:45:03 CEST 2019 

Dear all, I created a small example that reproduces my error below. It has to do with my use of module with  .constructor<const Rcpp::NumericVector &, int>() with Rcpp::NumericVector. I guess I’m not doing things the right way but since it is working on windows and used to work until now with my Mac … 

Thanks in advance for your help (below the simple test and the error obtained) 
Regards
Robin

#include <Rcpp.h>
using namespace Rcpp;

class MyModel
{
public:
  double a;
  ~MyModel();
  MyModel();
  MyModel(const Rcpp::NumericVector& ModelData, int temp);
};

RCPP_EXPOSED_CLASS(MyModel)
  
  MyModel::~MyModel() 
  {}
MyModel::MyModel() : a(0) 
{}
MyModel::MyModel(const Rcpp::NumericVector& ModelData, int temp) : a(0)
{}

RCPP_MODULE(MyModel){
  
  Rcpp::class_<MyModel>("MyModel")
  .constructor()
  .constructor<const Rcpp::NumericVector &, int>()
  ;
}


Compilation error : 

/usr/local/clang7/bin/clang++  -Wall -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Users/robin.girard/Documents/Code/Packages/test_modules/Test2/src" -I"/Users/robin.girard/Documents/Code/Packages/test_modules/Test2/src/../inst/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c test.cpp -o test.o
In file included from test.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:168:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/as.h:25:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/internal/Exporter.h:31:30: error: reference member 't' binds to a temporary object whose lifetime would be shorter than the lifetime of the constructed object
                    Exporter( SEXP x ) : t(x){}
                                           ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/as.h:87:41: note: in instantiation of member function 'Rcpp::traits::Exporter<const Rcpp::Vector<14, PreserveStorage> &>::Exporter' requested here
            ::Rcpp::traits::Exporter<T> exporter(x);
                                        ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/as.h:152:26: note: in instantiation of function template specialization 'Rcpp::internal::as<const Rcpp::Vector<14, PreserveStorage> &>' requested here
        return internal::as<T>(x, typename traits::r_type_traits<T>::r_category());
                         ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:58:13: note: in instantiation of function template specialization 'Rcpp::as<const Rcpp::Vector<14, PreserveStorage> &>' requested here
            as<U0>(args[0]),
            ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/module/Module_generated_class_constructor.h:91:29: note: in instantiation of member function 'Rcpp::Constructor_2<MyModel, const Rcpp::Vector<14, PreserveStorage> &, int>::get_new' requested here
        AddConstructor( new Constructor_2<Class,U0,U1> , valid, docstring ) ;
                            ^
test.cpp:26:4: note: in instantiation of function template specialization 'Rcpp::class_<MyModel>::constructor<const Rcpp::Vector<14, PreserveStorage> &, int>' requested here
  .constructor<const Rcpp::NumericVector &, int>()
   ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/internal/Exporter.h:35:9: note: reference member declared here
                    T t ;
1 error generated.
make: *** [test.o] Error 1
Error in Rcpp::sourceCpp("src/test.cpp") : 
  Error 1 occurred building shared library.



> Le 3 mai 2019 à 08:41, Robin GIRARD <robin.girard at mines-paristech.fr> a écrit :
> 
> I found a way to solve my RcppArmadillo problem here https://stackoverflow.com/questions/51761599/cannot-find-stdio-h <https://stackoverflow.com/questions/51761599/cannot-find-stdio-h>
> I don’t really understand what happened because I had the file. 
> The other error is still here
> Regards
> Robin
> 
>> Le 3 mai 2019 à 08:32, Robin GIRARD <robin.girard at mines-paristech.fr <mailto:robin.girard at mines-paristech.fr>> a écrit :
>> 
>> Dear Simon, 
>> 
>> **regarding RcppArmadillo build from source pb**  the config.log is attached and points the following error while checking something about cross  compilation.
>> In file included from conftest.cpp:9:
>> /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file not found
>> #include_next <stdio.h>
>> 
>> But this file exists. 
>> 
>> ** regarding my compilation error** it is obtained while trying to build the module file, when calling #include "Rcpp.h » (line 4 of file Client.hpp) 
>> /usr/local/clang7/bin/clang++  -Wall -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -std=c++11 -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mod_client.cc <http://mod_client.cc/> -o mod_client.o
>> 
>> In file included from mod_client.cc <http://mod_client.cc/>:1:
>> In file included from ../inst/include/Client.hpp:4:
>> In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
>> In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:168:
>> In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/as.h:25:
>> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/internal/Exporter.h:31:30: error: reference member 't' binds to a temporary object whose lifetime would be shorter than the lifetime of the constructed object
>>                     Exporter( SEXP x ) : t(x){}
>> 
>> Thanks in advance for your help
>> Regards
>> Robin
>> 
>> <config.log>
>> 
>>> Le 2 mai 2019 à 23:18, Simon Urbanek <simon.urbanek at R-project.org <mailto:simon.urbanek at R-project.org>> a écrit :
>>> 
>>> Robin,
>>> 
>>> this is unlikely a Mac issue, merely newer compilers give you better error handling pointing to issues in the code that may not have been detected before. If you post the code we can have a look.
>>> 
>>> Also check your tools - the RcppArmadillo error points out that your compiler setup is broken since it cannot create runnable executable. Check config.log for details.
>>> 
>>> Cheers,
>>> Simon
>>> 
>>> 
>>> 
>>>> On May 2, 2019, at 1:04 PM, Robin GIRARD <robin.girard at mines-paristech.fr <mailto:robin.girard at mines-paristech.fr>> wrote:
>>>> 
>>>> Dear all, avec a Mac update today I obtained the following error while compiling a package of mine using Rcpp : 
>>>> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/internal/Exporter.h:31:30: error: reference member 't' binds to a temporary object whose lifetime would be shorter than the lifetime of the constructed object
>>>>                    Exporter( SEXP x ) : t(x){}
>>>> 
>>>> I’m pretty sure this has something to do with Mac, I updated the Command line tool, I manage to compile simple examples with sourceRcpp (trying to follow instructions here http://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-macos/ <http://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-macos/>) I’m still trying to reproduce my error on a simple example. 
>>>> I have R 3.6 and clang7 installed. 
>>>> 
>>>> Another strange point (might be connected) is that when I try to install RcppArmadillo from source (as suggested in link above with install.packages("", type = "source »)) it gives something about cross compiling:
>>>> 
>>>> checking whether the C++ compiler works... yes
>>>> checking for C++ compiler default output file name... a.out
>>>> checking for suffix of executables... 
>>>> checking whether we are cross compiling... configure: error: in `/private/var/folders/zt/7cz1y9md79l_h08bbqymt4w9z8xlw7/T/Rtmpgi7WQZ/R.INSTALL4f4110aa3f/RcppArmadillo':
>>>> configure: error: cannot run C++ compiled programs.
>>>> If you meant to cross compile, use `--host'.
>>>> See `config.log' for more details
>>>> ERROR: configuration failed for package ‘RcppArmadillo’
>>>> 
>>>> 
>>>> Thanks in advance for your help
>>>> Regards
>>>> Robin
>>>> 
>>>> 
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>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel <https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel>
>>> 
>> 
> 
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