[R] [Rcpp-devel] Help with integrating R and c/c++

[Douglas Bates]

On Sat, Feb 19, 2011 at 12:56 AM, Rohit Pandey <rohitpandey576 at gmail.com> wrote:
> Hi Christopher/ Dirk,

> Thank you very much for your replys. I think the idea of using inline as you
> suggest is the best way to start off with using c++ with R. I went through
> your examples and also plenty I found on the net. I have been trying to run
> some of these over the past few days, but have consistently been getting
> this error message as soon as I run the 'cfunction' or 'cxxfunction'. For
> example, in the syntax that Dirk sent,
> R> library(inline) #Runs perfectly
>  R> src <- 'std::cout << "Hello C++_From_R World" << std::endl;
> return(Rcpp::wrap(42));' #Runs perfectly
>  R> rohit <- cxxfunction(signature(), src, plugin="Rcpp")
> Now, as soon as I run this line, R spills a whole lot of text out and gives
> an error and a warning:
> ERROR(s) during compilation: source code errors or compiler configuration
> errors!
> Program source:
>  1:
>  2: // includes from the plugin
>  3:
>  4: #include <Rcpp.h>
>  5:
>  6:
>  7: #ifndef BEGIN_RCPP
>  8: #define BEGIN_RCPP
>  9: #endif
>  10:
>  11: #ifndef END_RCPP
>  12: #define END_RCPP
>  13: #endif
>  14:
>  15: using namespace Rcpp;
>  16:
>  17:
>  18: // user includes
>  19:
>  20:
>  21: // declarations
>  22: extern "C" {
>  23: SEXP file59046688( ) ;
>  24: }
>  25:
>  26: // definition
>  27:
>  28: SEXP file59046688(  ){
>  29: BEGIN_RCPP
>  30: std::cout << "Hello C++_From_R World" << std::endl;
> return(Rcpp::wrap(42));
>  31: END_RCPP
>  32: }
>  33:
>  34:
> Error in compileCode(f, code, language = language, verbose = verbose) :
>  Compilation ERROR, function(s)/method(s) not created!
> In addition: Warning message:
> running command 'C:\PROGRA~1\R\R-212~1.1/bin/i386/R CMD SHLIB
> file59046688.cpp 2> file59046688.cpp.err.txt' had status 1
>
> The "file59046688.cpp 2"  changes every time I run a different function, but
> the problem seems to be the same.
>
> I installed and loaded the inline package (0.3.8) and then the Rcpp package
> (0.9.0). I also tried reversing the order in which I load these, but still
> no luck. I think if I can get just one of these programs to work, I will be
> on my way. Can any of you tell me what I might be doing wrong?
>
> For your question on what exacly I require, Christopher - I just need to use
> a while loop. I have always been able to substitute for loops with some of
> the apply functions in R, but can't seem to be able to replace the while
> with a more efficient function. But the things that are required inside the
> while loop, I have already implemented in R efficiently. So, I thought of
> transfering just the while loop to a language that is faster with loops.

What operating system and version of R are you using?  It would help
if you included the results of executing

sessionInfo()

in R.  More importantly, do you have the compiler tools installed and
configured?  You need to have certain tools installed on Windows or
Mac OS X before you can compile packages (as opposed to installing
pre-compiled binary packages).  Most Linux distributions assume that
their users are adults and provide them with the tools to compile
programs.

>
> Thanks in advance.
> On Mon, Feb 7, 2011 at 6:21 AM, Wray, Christopher <
> christopher.wray.10 at ucl.ac.uk> wrote:
>
>> As Dirk says, using "inline" makes it real simple to start and to prototype
>> code.
>>
>> You mention you have R functions you wish to "call" via Rcpp. Im not
>> certain I fully understand what you require here, but it is pretty simple to
>> pass R-side functions to C++ via Rcpp, and similarly its simple to send
>> compiled functions back to R-side as external pointers (and reuse them
>> elsewhere). Here is a toy example using a simple "user" function defined on
>> the R-side (user_F).
>>
>> This is evaluated in R, passed as a "function" parameter to compiled C++
>> function and evaluated there, and then a compiled version of the function is
>> passed back to R as an external pointer, which you can send back to the C
>> side and evaluate:
>>
>> <R> user_F=function(v){sum((1-v)*exp(-0.5*v))}
>>
>> cpp <- '
>> NumericVector numvec(xvec);
>> NumericVector RetVec;
>> Function userR_f(fun);
>> List ATR;
>> typedef SEXP (*h_ptr)(SEXP);
>> RetVec = userR_f(numvec);
>> ATR["Fn_ptr"]=XPtr<h_ptr> (new h_ptr(&fme));
>> ATR["Fn_VAL"]=RetVec;
>> return ATR;
>> '
>> inc<-'
>> using namespace Rcpp;
>> SEXP fme(SEXP x){
>> NumericVector xx(x);
>> NumericVector yy=(1-xx)*exp(-0.5*xx);
>> double Ans=sum(yy);
>> return wrap(Ans);
>> }
>> '
>> <R> FN_CSide <- cxxfunction(signature(xvec = "numeric", fun = "function"
>> ),cpp, , plugin = "Rcpp", includes = inc)
>>
>> cppP <- '
>> typedef SEXP (*h_ptr)(SEXP);
>> XPtr<h_ptr>p(x);
>> NumericVector yy(y);
>> yy=(*p)(yy);
>> return yy;
>> '
>> <R> px<-cxxfunction(signature(x = "externalptr", y = "numeric" ),cppP, ,
>> plugin = "Rcpp", includes = "using namespace Rcpp; ")
>>
>> <R> R_side=FN_CSide(seq(1,5),user_F)
>> <R> user_F(seq(1,5))
>> [1] -1.548486
>> <R> R_side
>> $Fn_ptr
>> <pointer: 0x0964c608>
>> $Fn_VAL
>> [1] -1.548486
>> <R> px(R_side$Fn_ptr,seq(1,5))
>> [1] -1.548486
>>
>> I've broken it out to make the logic explicit. The above is sloppy - and
>> makes no attempt to treat memory de/allocation/gc/protection issues (which
>> you should consider) especially if you pass objects around, but it does try
>> to show you how the mechanics work.
>>
>> Aside from looking up the Rcpp::sugar functionality used in places above,
>> you might also want to look at package "RcppArmadillo", if functions and
>> calculations involve linear algebra calcs/matrix operations. Hopefully this
>> gives you some food-for-thought to delve further into the
>> archives/documentation to find what you need.
>> chris
>>
>>
>>
>> ________________________________________
>> From: rcpp-devel-bounces at r-forge.wu-wien.ac.at [
>> rcpp-devel-bounces at r-forge.wu-wien.ac.at] on behalf of Dirk Eddelbuettel [
>> edd at debian.org]
>> Sent: 06 February 2011 18:18
>> To: Dirk Eddelbuettel
>> Cc: Rohit Pandey; rcpp-devel
>> Subject: Re: [Rcpp-devel] [R] Help with integrating R and c/c++
>>
>> [ Now resending to rcpp-devel as I had said below I would --Dirk ]
>>
>> On 6 February 2011 at 20:58, Rohit Pandey wrote:
>> | Hi,
>> |
>> | I have been using R for close to two years now and have grown quite
>> | comfortable with the language. I am presently trying to implement an
>> | optimization routine in R (Newton Rhapson). I have some R functions that
>> | calculate the gradient and hessian (pre requisite matrices) fairly
>> | efficiently. Now, I have to call this function iteratively until some
>> | convergance criterion is reached. I think the standard method of doing
>> this
>> | in most programming languages is a while loop. However, I know R can get
>> | pretty slow when you use loops. In order to make this efficient, I want
>> to
>> | transfer this part of my code to a more efficient programming language
>> like
>> | c++ or c. However, I have been trying to learn this all day without any
>> | luck. I found a package called Rcpp that makes this easier. However, it
>> | seems some functional knowledge of writing R packages is a pre requisite.
>> I
>>
>> What gave you that impression?
>>
>> Here is a counter-example, using the packages inline (for cxxfunction) and
>> Rcpp:
>>
>>  R> library(inline)
>>  R> src <- 'std::cout << "Hello C++_From_R World" << std::endl;
>> return(Rcpp::wrap(42));'
>>  R> rohit <- cxxfunction(signature(), src, plugin="Rcpp")
>>  R> rohit()
>>  Hello C++_From_R World
>>  [1] 42
>>  R>
>>
>> This compiled, linked and loaded a C++ routine built from the two-statement
>> program submitted as character variable.
>>
>> The Rcpp documentation, including its eight vignettes, is full of other
>> examples. Start with Rcpp-introduction and maybe the Rcpp-FAQ.
>>
>> | tried to follow the standard manual for doing this, but could not find a
>> | simple example to get me started. I know I am supposed to make a cpp file
>> | and put it some where before it can be called from R, but I'm confused as
>> to
>> | how this can be done.
>> |
>> | My requirement is to start with a parameter vector, update it according
>> to
>> | the gradient and hessian, check if the parameter satisfies some
>> convergance
>> | criterion and continue doing this until it does. Is there a way to
>> | efficiently do this through an R function (replicate?). The problem is
>> that
>> | the number of iterations is not fixed. If there is no function in R, is
>> | there a way I can quickly use Rcpp or some thing to have this last part
>> of
>> | my code in a C or C++ program which repeatedly calls my R functions for
>> | updating the parameters?
>>
>> Give the example above a first try, and then read some more. The archives
>> of
>> the rcpp-devel (CC'ed; post there for follow-ups after subscribing) list
>> are
>> full of examples, and the CRAN page for Rcpp lists almost two dozen other
>> packages using Rcpp giving you plenty of examples should you want to write
>> a
>> package using Rcpp. Several of these packages do optimization giving you
>> examples of you to pass parameters etc pp.
>>
>> Hope this helps, Dirk
>>
>> |
>> | --
>> | Thanks in advance,
>> | Rohit
>> | Mob: 91 9819926213
>> |
>> |       [[alternative HTML version deleted]]
>> |
>> | ______________________________________________
>> | R-help at r-project.org mailing list
>> | https://stat.ethz.ch/mailman/listinfo/r-help
>> | PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
>> | and provide commented, minimal, self-contained, reproducible code.
>>
>> --
>> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
>> _______________________________________________
>> Rcpp-devel mailing list
>> Rcpp-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>
>
>
>
> --
> Thanks,
> Rohit
> Mob: 91 9819926213
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>