[R-sig-dyn-mod] deSolve with compiled code and varying size of parms

[Rampal S. Etienne]

The errors with the code are resolved by running the following line in R:

Sys.setenv( "PKG_CXXFLAGS"="-std=c++11" )


The last questions remains, however: how does the parameter N in sys get
specified?

RSE.

On 29-3-2017 9:50, Rampal S. Etienne wrote:
>
> Thanks for the quick reply. However, when I run this code, I get loads
> of errors. See below. Similar errors are obtained when running the
> examples in the odeintr documentation (e.g. logistic).
>
> Also, how does the parameter N in sys get specified?
>
> RSE
>
>
> g++ -m64 -std=c++0x -I"C:/PROGRA~1/R/R-devel/include" -DNDEBUG     -I"C:/PROGRA~1/R/R-devel/library/Rcpp/include" -I"C:/PROGRA~1/R/R-devel/library/odeintr/include" -I"C:/PROGRA~1/R/R-devel/library/BH/include" -I"C:/Users/p223208/AppData/Local/Temp/RtmpCsE4eO"  -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c file3670a102674.cpp -o file3670a102674.o
> In file included from C:/PROGRA~1/R/R-devel/library/BH/include/boost/fusion/view/zip_view/zip_view.hpp:13:0,
>                  from C:/PROGRA~1/R/R-devel/library/BH/include/boost/fusion/view/zip_view.hpp:12,
>                  from C:/PROGRA~1/R/R-devel/library/BH/include/boost/fusion/include/zip_view.hpp:11,
>                  from C:/PROGRA~1/R/R-devel/library/BH/include/boost/numeric/odeint/util/resize.hpp:26,
>                  from C:/PROGRA~1/R/R-devel/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
>                  from C:/PROGRA~1/R/R-devel/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
>                  from C:/PROGRA~1/R/R-devel/library/BH/include/boost/numeric/odeint.hpp:25,
>                  from file3670a102674.cpp:10:
> C:/PROGRA~1/R/R-devel/library/BH/include/boost/fusion/support/unused.hpp: In member function 'const boost::fusion::unused_type& boost::fusion::unused_type::operator=(const boost::fusion::unused_type&) const':
> C:/PROGRA~1/R/R-devel/library/BH/include/boost/fusion/support/unused.hpp:57:9: error: 'this' is not a potential constant expression
> C:/PROGRA~1/R/R-devel/library/BH/include/boost/fusion/support/unused.hpp: At global scope:
> C:/PROGRA~1/R/R-devel/library/BH/include/boost/fusion/support/unused.hpp:67:39: error: both 'const' and 'constexpr' cannot be used here
> file3670a102674.cpp: In function 'void odeintr::sys(odeintr::state_type, odeintr::state_type&, double)':
> file3670a102674.cpp:39:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
> file3670a102674.cpp:42:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
> file3670a102674.cpp: In function 'void odeintr::obs(odeintr::state_type, double)':
> file3670a102674.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
> file3670a102674.cpp: In function 'Rcpp::List test_get_output()':
> file3670a102674.cpp:70:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
> file3670a102674.cpp:72:36: error: 'to_string' is not a member of 'std'
> file3670a102674.cpp:72:36: note: suggested alternative:
> C:/PROGRA~1/R/R-devel/library/BH/include/boost/units/units_fwd.hpp:61:31: note:   'boost::units::to_string'
> file3670a102674.cpp:72:56: error: unable to deduce 'auto' from '<expression error>'
> file3670a102674.cpp: In function 'void test_set_state(Rcpp::NumericVector)':
> file3670a102674.cpp:85:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
> C:/PROGRA~1/R/R-devel/library/odeintr/include/utils.h: At global scope:
> C:/PROGRA~1/R/R-devel/library/odeintr/include/utils.h:30:1: warning: 'double odeintr::laplace2D(const state_type&, int, int)' defined but not used [-Wunused-function]
> make: *** [file3670a102674.o] Error 1
> Warning message:
> running command 'make -f "C:/PROGRA~1/R/R-devel/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-devel/share/make/winshlib.mk" CXX='$(CXX1X) $(CXX1XSTD)' CXXFLAGS='$(CXX1XFLAGS)' CXXPICFLAGS='$(CXX1XPICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX1XLDFLAGS)' SHLIB_LD='$(SHLIB_CXX1XLD)' SHLIB="sourceCpp_1.dll" WIN=64 TCLBIN=64 OBJECTS="file3670a102674.o"' had status 2 
> Error in Rcpp::sourceCpp(code = code, env = env, ...) : Error 1
> occurred building shared library. > test_set_params(rnorm(10)) Error:
> could not find function "test_set_params" > x0 = rep(1, 10) > res =
> test(x0, 5) Error: could not find function "test"
>
> On 28-3-2017 22:37, Tim Keitt wrote:
>> On Tue, Mar 28, 2017 at 3:14 PM, Daniel Kaschek <
>> daniel.kaschek at physik.uni-freiburg.de> wrote:
>>
>>> By the way, there are some packages around working with deSolve and
>>> autogenerating C code or FORTRAN code, e.g., cOde and rodeo.
>>>
>> Here's an example in odeintr:
>>
>> library(odeintr)
>>> sys = '
>>>   for (int i = 0; i != N; ++i)
>>>   {
>>>     dxdt[i] = 0;
>>>     for (int j = 0; j != N; ++j)
>>>       dxdt[i] += pars[j] * x[j];
>>>   }
>>> '
>>> n_pars = 10
>>> compile_sys("test", sys, n_pars, sys_dim = n_pars)
>>> test_set_params(rnorm(10))
>>> x0 = rep(1, 10)
>>> res = test(x0, 5)
>> The dimension is currently set at compile time, but that would be easy to
>> change.
>>
>> THK
>>
>> http://www.keittlab.org/
>>
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>>
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>


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