A simple hello world program using Stan Math Error

Ivan Aliaga

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Nov 27, 2016, 11:10:40 PM11/27/16

to Stan users mailing list

Hello every world Stan R.

I have problem with Rstan and package Rcpp when installation is newbie

i instaled the follow packages

>install.packages("StanHeader",dep=TRUE)
>install.packages("rstantools",dep=TRUE)
>devtools::install_github("stan-dev/rstan", ref = "develop", subdir = "rstan/rstan", build_vignettes = TRUE, dependencies = TRUE)

a simple "CodeStanPrueba.cpp" file is.

#include <stan/math.hpp>

#include <iostream>

// [[Rcpp::export]]

int simple() {

std::cout << "log normal(1 | 2, 3)="

<< stan::math::normal_log(1, 2, 5)

<< std::endl;

}

when execute

>Rcpp::sourceCpp("CodeStanPrueba.cpp")

C:/Rtools/mingw_64/bin/g++ -I"C:/PROGRA~1/R/R-33~1.2/include" -DNDEBUG -I"C:/Users/IVANAL~1/DOCUME~1/R/WIN-LI~1/3.3/Rcpp/include" -I"C:/Users/IVANAL~1/Desktop/BAYESI~1" -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -lrt -c CodeStanPrueba.cpp -o CodeStanPrueba.o

CodeStanPrueba.cpp:1:25: fatal error: stan/math.hpp: No such file or directory

#include <stan/math.hpp>

^

compilation terminated.

make: *** [CodeStanPrueba.o] Error 1

Warning message:

comando ejecutado 'make -f "C:/PROGRA~1/R/R-33~1.2/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-33~1.2/share/make/winshlib.mk" -f "C:\Users\IVAN ALIAGA\Documents/.R/Makevars" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="sourceCpp_4.dll" WIN=64 TCLBIN=64 OBJECTS="CodeStanPrueba.o"' tiene estatus 2

Error in Rcpp::sourceCpp("CodeStanPrueba.cpp") :

Error 1 occurred building shared library.

> version

platform x86_64-w64-mingw32

arch x86_64

os mingw32

system x86_64, mingw32

status

major 3

minor 3.2

year 2016

month 10

day 31

svn rev 71607

language R

version.string R version 3.3.2 (2016-10-31)

nickname Sincere Pumpkin Patch

> system("g++ -v")

Using built-in specs.

COLLECT_GCC=c:\Rtools\mingw_32\bin\G__~1.EXE

COLLECT_LTO_WRAPPER=c:/Rtools/mingw_32/bin/../libexec/gcc/i686-w64-mingw32/4.9.3/lto-wrapper.exe

Target: i686-w64-mingw32

Configured with: ../../../src/gcc-4.9.3/configure --host=i686-w64-mingw32 --build=i686-w64-mingw32 --target=i686-w64-mingw32 --prefix=/mingw32 --with-sysroot=/home/Jeroen/mingw-gcc-4.9.3/i686-493-posix-dwarf-rt_v3-s/mingw32 --with-gxx-include-dir=/mingw32/i686-w64-mingw32/include/c++ --enable-static --disable-shared --disable-multilib --enable-languages=c,c++,fortran,lto --enable-libstdcxx-time=yes --enable-threads=posix --enable-libgomp --enable-libatomic --enable-lto --enable-graphite --enable-checking=release --enable-fully-dynamic-string --enable-version-specific-runtime-libs --disable-sjlj-exceptions --with-dwarf2 --disable-isl-version-check --disable-cloog-version-check --disable-libstdcxx-pch --disable-libstdcxx-debug --enable-bootstrap --disable-rpath --disable-win32-registry --disable-nls --disable-werror --disable-symvers --with-gnu-as --with-gnu-ld --with-arch=i686 --with-tune=generic --with-libiconv --with-system-zlib --with-gmp=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --with-mpfr=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --with-mpc=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --with-isl=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --with-cloog=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --enable-cloog-backend=isl --with-pkgversion='i686-posix-dwarf, Built by MinGW-W64 project' --with-bugurl=http://sourceforge.net/projects/mingw-w64 CFLAGS='-O2 -pipe -I/home/Jeroen/mingw-gcc-4.9.3/i686-493-posix-dwarf-rt_v3-s/mingw32/opt/include -I/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-zlib-static/include -I/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static/include' CXXFLAGS='-O2 -pipe -I/home/Jeroen/mingw-gcc-4.9.3/i686-493-posix-dwarf-rt_v3-s/mingw32/opt/include -I/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-zlib-static/include -I/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static/include' CPPFLAGS= LDFLAGS='-pipe -L/home/Jeroen/mingw-gcc-4.9.3/i686-493-posix-dwarf-rt_v3-s/mingw32/opt/lib -L/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-zlib-static/lib -L/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static/lib -Wl,--large-address-aware'

Thread model: posix

gcc version 4.9.3 (i686-posix-dwarf, Built by MinGW-W64 project)

> sessionInfo()

R version 3.3.2 (2016-10-31)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 8.1 x64 (build 9600)

locale:

[1] LC_COLLATE=Spanish_Bolivia.1252 LC_CTYPE=Spanish_Bolivia.1252

[3] LC_MONETARY=Spanish_Bolivia.1252 LC_NUMERIC=C

[5] LC_TIME=Spanish_Bolivia.1252

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:

[1] rstan_2.12.1 StanHeaders_2.12.0-1 ggplot2_2.2.0

loaded via a namespace (and not attached):

[1] colorspace_1.2-7 scales_0.4.1 assertthat_0.1 lazyeval_0.2.0

[5] plyr_1.8.4 tools_3.3.2 inline_0.3.14 gtable_0.2.0

[9] tibble_1.2 gridExtra_2.2.1 Rcpp_0.12.8 grid_3.3.2

[13] stats4_3.3.2 munsell_0.4.3

I think in https://github.com/stan-dev/math the result is:

> cd /path/to/foo
> clang++ -I /path/to/stan-math -I /path/to/Eigen -I /path/to/boost foo.cpp  -I /path/to/cvodes
> ./a.out
log normal(1 | 2, 3)=-2.07311

Ben Goodrich

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Nov 27, 2016, 11:36:06 PM11/27/16

to Stan users mailing list

On Sunday, November 27, 2016 at 11:10:40 PM UTC-5, Ivan Aliaga wrote:

a simple "CodeStanPrueba.cpp" file is.

#include <stan/math.hpp>
#include <iostream>
// [[Rcpp::export]]
int simple() {
std::cout << "log normal(1 | 2, 3)="
<< stan::math::normal_log(1, 2, 5)
<< std::endl;
}

You need

// [[Rcpp::depends(rstan)]]

at the top (and to actually return an int).

Ben

Ivan Aliaga

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Nov 28, 2016, 11:17:37 AM11/28/16

to Stan users mailing list

Sorry, ok thanks, but a modify file CodeStanPrueba.cpp

#include <stan/math.hpp>

#include <iostream>

// [[Rcpp::export]]

// [[Rcpp::depends(rstan)]]

int simple() {

std::cout << "log normal(1 | 2, 3)="

<< stan::math::normal_log(1, 2, 3)

<< std::endl;

}

>Rcpp::sourceCpp("CodeStanPrueba.cpp")

C:/Rtools/mingw_64/bin/g++ -I"C:/PROGRA~1/R/R-33~1.2/include" -DNDEBUG -I"C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/Rcpp/include/" -I"C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/RcppEigen/include/" -I"C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/RcppEigen/include/unsupported" -I"C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/rstan/include/boost_not_in_BH" -I"C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/BH/include" -I"C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/src/" -I"C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/" -I"C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I"C:/Users/IVANAL~1/DOCUME~1/R/WIN-LI~1/3.3/Rcpp/include" -I"C:/Users/IVANAL~1/DOCUME~1/R/WIN-LI~1/3.3/rstan/include" -I"C:/Users/IVANAL~1/Desktop/BAYESI~1" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c CodeStanPrueba.cpp -o CodeStanPrueba.o

In file included from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/BH/include/boost/multi_array/base.hpp:28:0,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/BH/include/boost/multi_array.hpp:21,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/BH/include/boost/numeric/odeint/util/multi_array_adaption.hpp:29,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/BH/include/boost/numeric/odeint.hpp:61,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:13,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math/prim/arr.hpp:36,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math/prim/mat.hpp:235,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math/rev/mat.hpp:9,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math.hpp:4,

from CodeStanPrueba.cpp:1:

C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/BH/include/boost/multi_array/concept_checks.hpp: In static member function 'static void boost::multi_array_concepts::detail::idgen_helper<N>::call(Array&, const IdxGen&, Call_Type)':

C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/BH/include/boost/multi_array/concept_checks.hpp:42:43: warning: typedef 'index_range' locally defined but not used [-Wunused-local-typedefs]

typedef typename Array::index_range index_range;

^

C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/BH/include/boost/multi_array/concept_checks.hpp:43:37: warning: typedef 'index' locally defined but not used [-Wunused-local-typedefs]

typedef typename Array::index index;

^

C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/BH/include/boost/multi_array/concept_checks.hpp: In static member function 'static void boost::multi_array_concepts::detail::idgen_helper<0ull>::call(Array&, const IdxGen&, Call_Type)':

C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/BH/include/boost/multi_array/concept_checks.hpp:53:43: warning: typedef 'index_range' locally defined but not used [-Wunused-local-typedefs]

typedef typename Array::index_range index_range;

^

C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/BH/include/boost/multi_array/concept_checks.hpp:54:37: warning: typedef 'index' locally defined but not used [-Wunused-local-typedefs]

typedef typename Array::index index;

^

CodeStanPrueba.cpp: In function 'int simple()':

CodeStanPrueba.cpp:10:1: warning: no return statement in function returning non-void [-Wreturn-type]

}

^

CodeStanPrueba.cpp: At global scope:

CodeStanPrueba.cpp:15:50: error: expected primary-expression before 'simple'

RcppExport SEXP sourceCpp_1_[[Rcpp::depends(SEXP simple(SEXP) {

^

CodeStanPrueba.cpp:19:43: warning: c++11 attributes only available with -std=c++11 or -std=gnu++11

Rcpp::traits::input_parameter< rstan)]] int >::type simple((simple(SEXP);

^

CodeStanPrueba.cpp:19:45: error: expected initializer before 'int'

Rcpp::traits::input_parameter< rstan)]] int >::type simple((simple(SEXP);

^

CodeStanPrueba.cpp:20:5: error: 'rcpp_result_gen' does not name a type

rcpp_result_gen = Rcpp::wrap([[Rcpp::depends(simple());

^

CodeStanPrueba.cpp:21:5: error: expected unqualified-id before 'return'

return rcpp_result_gen;

^

In file included from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/Rcpp/include/Rcpp/r/headers.h:50:0,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/Rcpp/include/RcppCommon.h:29,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/Rcpp/include/Rcpp.h:27,

from CodeStanPrueba.cpp:12:

C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/Rcpp/include/Rcpp/macros/macros.h:38:5: error: expected declaration before '}' token

} \

^

C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/Rcpp/include/Rcpp/macros/macros.h:60:18: note: in expansion of macro 'VOID_END_RCPP'

#define END_RCPP VOID_END_RCPP return R_NilValue;

^

CodeStanPrueba.cpp:22:1: note: in expansion of macro 'END_RCPP'

END_RCPP

^

In file included from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7:0,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math/rev/core.hpp:34,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math/rev/mat.hpp:4,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math.hpp:4,

from CodeStanPrueba.cpp:1:

C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:65:18: warning: 'stan::math::NEGATIVE_EPSILON' defined but not used [-Wunused-variable]

const double NEGATIVE_EPSILON

^

In file included from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math/rev/core.hpp:42:0,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math/rev/mat.hpp:4,

from C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math.hpp:4,

from CodeStanPrueba.cpp:1:

C:/Users/IVAN ALIAGA/Documents/R/win-library/3.3/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:17: warning: 'void stan::math::set_zero_all_adjoints()' defined but not used [-Wunused-function]

static void set_zero_all_adjoints() {

^

make: *** [CodeStanPrueba.o] Error 1

Warning message:

comando ejecutado 'make -f "C:/PROGRA~1/R/R-33~1.2/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-33~1.2/share/make/winshlib.mk" -f "C:\Users\IVAN ALIAGA\Documents/.R/Makevars" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="sourceCpp_2.dll" WIN=64 TCLBIN=64 OBJECTS="CodeStanPrueba.o"' tiene estatus 2

Error in Rcpp::sourceCpp("CodeStanPrueba.cpp") :

Error 1 occurred building shared library.

Ben Goodrich

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Nov 28, 2016, 1:32:10 PM11/28/16

to Stan users mailing list

On Monday, November 28, 2016 at 11:17:37 AM UTC-5, Ivan Aliaga wrote:

Sorry, ok thanks, but a modify file CodeStanPrueba.cpp

#include <stan/math.hpp>
#include <iostream>

// [[Rcpp::export]]
// [[Rcpp::depends(rstan)]]
int simple() {
std::cout << "log normal(1 | 2, 3)="
<< stan::math::normal_log(1, 2, 3)
<< std::endl;
}

// [[Rcpp::depends(rstan)]]

#include <stan/math.hpp>
#include <iostream>
// [[Rcpp::export]]
int simple() {
std::cout << "log normal(1 | 2, 3)="
<< stan::math::normal_log(1, 2, 5)
<< std::endl;

return 0;
}

Ben

Ivan Aliaga

unread,

Dec 9, 2016, 10:00:01 AM12/9/16

to Stan users mailing list

Thanks Ben very good!!!

But it is normal to see these messages, of course the result is good as published.