# Struggling with user-defined custom c++ function for binning real data into sequence of integer counts

**URL:** <https://discourse.mc-stan.org/t/struggling-with-user-defined-custom-c-function-for-binning-real-data-into-sequence-of-integer-counts/27448>\
**Category:** Interfaces\
**Tags:** user-defined-functions\
**Created:** [May 12, 2022, 11:16am UTC](https://discourse.mc-stan.org/t/struggling-with-user-defined-custom-c-function-for-binning-real-data-into-sequence-of-integer-counts/27448 "2022-05-12T11:16:04Z")\
**Posts on this page:** 8\
**Page:** 1

<div class="post-metadata">

**Author:** ![wcc](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/wcc/32/14171_2.png) [@wcc](https://discourse.mc-stan.org/u/wcc)\
**Post date:** [May 12, 2022, 11:16am UTC](https://discourse.mc-stan.org/t/struggling-with-user-defined-custom-c-function-for-binning-real-data-into-sequence-of-integer-counts/27448/1 "2022-05-12T11:16:04Z")

</div>

In brief, I’m trying to write a custom c++ function that takes a vector of reals and returns an array of counts given some parameters for data binning (start, end, bin-width). I’m new to c++ and to Stan and will be using rstan to implement various models that will make use of this counting function. In part, I’m also just using this task as a way to learn rstan/Stan/c++ and build experience designing highly customized Stan models. I’m now encountering a parsing error that I can’t figure out and I would appreciate some help (and any suggestions for improvements on any of the code below).

To begin, the error. In an R session I’m calling a script (see below) that builds a Stan model in order to simply test a custom c++ function (also below). The R code is stored in “count2stan.R”, and the c++ function definition is in “stancount.cpp”. When called, the R script produces the following error:

> source(“./count2stan.R”)  
> SYNTAX ERROR, MESSAGE(S) FROM PARSER:  
> error in ‘model10333a7f6ac4fb\_counting’ at line 3, column 4

* * *

```
 1: 
 2: functions {
 3: array[] int count( vector somereals,
       ^
 4: real minimum,

```

* * *

PARSER EXPECTED: “}”  
Error in stanc(file = file, model\_code = model\_code, model\_name = model\_name, :  
failed to parse Stan model ‘counting’ due to the above error.

Now the relevant code (though, see attached for files so you don’t have to copy-n-paste).  
[count2stan.R](https://discourse.mc-stan.org/uploads/short-url/9azu11HMmhlTMiw3qhNGU2hq7Q4.R) (1.1 KB)  
[stancount.cpp](https://discourse.mc-stan.org/uploads/short-url/zP2tqdvHCwipzlP5J6mieQSBCnb.cpp) (722 Bytes)

R script:

```no-highlight
library(rstan)

model_code <-
'
functions {
    array[] int count( vector somereals,
                    real minimum,
                    real maximum,
                    real delta );
}
data {
    int N;
    int Nbins;
    vector[N] somereals;
    real minimum;
    real maximum;
    real delta;
}
model {}
generated quantities {
    int y[Nbins] = count(somereals, minimum, maximum, delta);
}
'

somereals = c(1, 2, 3.5, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14.99, 15.7, 16, 17, 24, 26)
N = length(somereals)
minimum = 5
maximum = 25
delta = 5
Nbins = floor((maximum - minimum) / delta)

mydata <- list(
    somereals = somereals,
    N = N,
    minimum = minimum,
    maximum = maximum,
    delta = delta,
    Nbins = Nbins
)

stancount = stan_model(model_code = model_code,
                        model_name = "counting",
                        allow_undefined = TRUE,
                        includes = paste0('\n#include "',
                                        file.path(getwd(), 'stancount.cpp'),
                                        '"\n'))

fit <- sampling(stancount, data = mydata)

#try(readLines(stanc(model_code=model_code, allow_undefined=T)$cppcode))

```

And CPP:

```no-highlight
#include <stan/math.hpp>

Eigen::Matrix<typename boost::math::tools::promote_args<T0 __, T1__ , T2 __, T3__ >::type, Eigen::Dynamic, 1>
count(const Eigen::Matrix<T0__, Eigen::Dynamic, 1>& invec,
          const T1__& minimum,
          const T2__& maximum,
          const T3 __& delta, std::ostream* pstream__ )
{
    int invec_size = invec.size();
    int cntvec_size = floor((maximum - minimum) / delta);
    Eigen::VectorXi cntvec(cntvec_size) = Eigen::VectorXi::Zero(); //vector<int> cntvec(cntvec_size, 0);
    for(int i=0; i<invec_size; i++){
        if(invec[i] >= minimum && invec[i] < maximum){
            int idx = floor((invec[i] - minimum) / delta);
            cntvec[idx]++;
        }
    }
    return cntvec;
}

```

The parser accepts the Stan function declaration if I use “vector” or “int” as the return type, but throws the aforementioned error when using “array int”. With “vector” as the return type, I was able to call the following in order to see the c++ code generated and try to match my custom function signature to Stan’s c++ code,

```no-highlight
try(readLines(stanc(model_code=model_code, allow_undefined=T)$cppcode))

```

I got this from “[Interfacing with External C++ Code • rstan](https://mc-stan.org/rstan/articles/external.html)” and have been trying to follow that guide.

Any help here would be greatly appreciated!

Operating System: Ubuntu 20.04  
Interface Version: latest rstan  
Compiler/Toolkit: gcc

Sincerely,  
Chris

---

<div class="post-metadata">

**Author:** ![maxbiostat](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/maxbiostat/32/1326_2.png) [@maxbiostat](https://discourse.mc-stan.org/u/maxbiostat)\
**Post date:** [May 12, 2022, 11:17am UTC](https://discourse.mc-stan.org/t/struggling-with-user-defined-custom-c-function-for-binning-real-data-into-sequence-of-integer-counts/27448/2 "2022-05-12T11:17:16Z")

</div>

@andrjohns

---

<div class="post-metadata">

**Author:** ![WardBrian](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/wardbrian/32/12078_2.png) [@WardBrian](https://discourse.mc-stan.org/u/WardBrian)\
**Post date:** [May 12, 2022, 1:51pm UTC](https://discourse.mc-stan.org/t/struggling-with-user-defined-custom-c-function-for-binning-real-data-into-sequence-of-integer-counts/27448/3 "2022-05-12T13:51:23Z")

</div>

By “latest RStan” do you mean the version available on CRAN? If so, this version is quite old and will not accept the `array` keyword-syntax. You will have to try the older syntax, `int[] count (...`

---

<div class="post-metadata">

**Author:** ![wcc](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/wcc/32/14171_2.png) [@wcc](https://discourse.mc-stan.org/u/wcc)\
**Post date:** [May 12, 2022, 2:10pm UTC](https://discourse.mc-stan.org/t/struggling-with-user-defined-custom-c-function-for-binning-real-data-into-sequence-of-integer-counts/27448/4 "2022-05-12T14:10:10Z")

</div>

Yes, I should have been clearer. Sorry about that! I installed from CRAN with install.packages(). I’ll try the older syntax, and maybe try installing the latest dev version of Stan instead of using CRAN.

---

<div class="post-metadata">

**Author:** ![WardBrian](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/wardbrian/32/12078_2.png) [@WardBrian](https://discourse.mc-stan.org/u/WardBrian)\
**Post date:** [May 12, 2022, 2:55pm UTC](https://discourse.mc-stan.org/t/struggling-with-user-defined-custom-c-function-for-binning-real-data-into-sequence-of-integer-counts/27448/5 "2022-05-12T14:55:38Z")

</div>

If you want to try using the newer versions, you can find instructions here: [Rstan Versioning - #2 by rok\_cesnovar](https://discourse.mc-stan.org/t/rstan-versioning/26515/2)

---

<div class="post-metadata">

**Author:** ![wcc](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/wcc/32/14171_2.png) [@wcc](https://discourse.mc-stan.org/u/wcc)\
**Post date:** [May 13, 2022, 8:32am UTC](https://discourse.mc-stan.org/t/struggling-with-user-defined-custom-c-function-for-binning-real-data-into-sequence-of-integer-counts/27448/6 "2022-05-13T08:32:37Z")

</div>

Okay it’s compiling now. Thanks for the help. I installed the newer version and fixed up my c++ after reading [Interfacing with External C++ Code](https://cran.r-project.org/web/packages/rstan/vignettes/external.html) a bit more carefully.

But, I’m now getting a DLL error when I try to call the new c++ function. See attached here for the source,

[count2stan.R](https://discourse.mc-stan.org/uploads/short-url/npQlUOCS8T4w9tJ5vcYYpr3Z5kv.R) (1.2 KB)  
[stancount.cpp](https://discourse.mc-stan.org/uploads/short-url/ndlmIvOodRZW8MhwVThYVRGhoXt.cpp) (498 Bytes)

And here’s the error,

```nohighlight
make would use
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I"/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include/" -I"/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/RcppEigen/include/" -I"/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/RcppEigen/include/unsupported" -I"/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/BH/include" -I"/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/include/src/" -I"/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/include/" -I"/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/RcppParallel/include/" -I"/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -include '/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c file118f9e2f8fd9ba.cpp -o file118f9e2f8fd9ba.o
if test "zfile118f9e2f8fd9ba.o" != "z"; then \
  echo g++ -std=gnu++14 -shared -L"/usr/lib/R/lib" -Wl,-Bsymbolic-functions -Wl,-z,relro -o file118f9e2f8fd9ba.so file118f9e2f8fd9ba.o '/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/rstan/lib//libStanServices.a' -L'/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/lib/' -lStanHeaders -L'/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/RcppParallel/lib/' -ltbb -L"/usr/lib/R/lib" -lR; \
  g++ -std=gnu++14 -shared -L"/usr/lib/R/lib" -Wl,-Bsymbolic-functions -Wl,-z,relro -o file118f9e2f8fd9ba.so file118f9e2f8fd9ba.o '/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/rstan/lib//libStanServices.a' -L'/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/lib/' -lStanHeaders -L'/home/carleton/R/x86_64-pc-linux-gnu-library/4.2/RcppParallel/lib/' -ltbb -L"/usr/lib/R/lib" -lR; \
fi
Error in dyn.load(libLFile) : 
  unable to load shared object '/tmp/RtmpVPnwCa/file118f9e2f8fd9ba.so':
  /tmp/RtmpVPnwCa/file118f9e2f8fd9ba.so: undefined symbol: _ZN38model118f9e7749f0af_counting_namespace5countIN5Eigen6MatrixIdLin1ELi1ELi0ELin1ELi1EEEdddEESt6vectorIiSaIiEERKT_RKT0_RKT1_RKT2_PSo

```

If I edit the model\_code so that no calls to count() are made, the compilation finishes with no errors. Here’s the error-free version,

```nohighlight
model_code <-
'
functions {
    array[] int count( vector rls,
                    real minimum,
                    real maximum,
                    real delta );
}
data {
    int N;
    int Nbins;
    vector[N] somereals;
    real minimum;
    real maximum;
    real delta;
}
transformed data {
    print(somereals);
    array[Nbins] int y;
    print(y);
}
model {}
generated quantities {}
'

```

Any ideas where to go from here?

---

<div class="post-metadata">

**Author:** ![WardBrian](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/wardbrian/32/12078_2.png) [@WardBrian](https://discourse.mc-stan.org/u/WardBrian)\
**Post date:** [May 13, 2022, 2:17pm UTC](https://discourse.mc-stan.org/t/struggling-with-user-defined-custom-c-function-for-binning-real-data-into-sequence-of-integer-counts/27448/7 "2022-05-13T14:17:44Z")

</div>

At this point I’m going to defer to @andrjohns @hsbadr

---

<div class="post-metadata">

**Author:** ![wcc](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/wcc/32/14171_2.png) [@wcc](https://discourse.mc-stan.org/u/wcc)\
**Post date:** [May 16, 2022, 7:46am UTC](https://discourse.mc-stan.org/t/struggling-with-user-defined-custom-c-function-for-binning-real-data-into-sequence-of-integer-counts/27448/8 "2022-05-16T07:46:02Z")

</div>

I think I have made some progress again, but again got stuck. To move forward, I tried explicitly referring to cmath::floor() instead of just calling floor() in the cpp file. Again, I’ve included here the most recent code:

[count2stan.R](https://discourse.mc-stan.org/uploads/short-url/npQlUOCS8T4w9tJ5vcYYpr3Z5kv.R) (1.2 KB)  
[stancount.cpp](https://discourse.mc-stan.org/uploads/short-url/lz3aBE3xFAFP95wFFfold4j7T48.cpp) (513 Bytes)

That seems to have resolved the previous error (“undefined symbol”). Now the error I’m receiving is,

```nohighlight
Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) : 
  /home/carleton/R/x86_64-pc-linux-gnu-library/4.2/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::evaluator(const XprType&) [with Lhs = Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Rhs = Eigen::Matrix<double, -1, 1>; int Options = 0; Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::XprType = Eigen::Product<Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>, Eigen::Matrix<double, -1, 1>, 0>]’/ho

```

I get this error as well when running the examples from [Interfacing with External C++ Code](https://cran.r-project.org/web/packages/rstan/vignettes/external.html). So, I’m guessing there’s some problem with the way my system is set up. The following seems to execute without error,

```nohighlight
example(stan_model, package = "rstan", run.dontrun = TRUE)

```

so I’m guessing there’s just some problem with trying to use external c++ code and it must have something to do with my configuration specifically (since I’m assuming the examples in [Interfacing with External C++ Code](https://cran.r-project.org/web/packages/rstan/vignettes/external.html) run for other people.

Any suggestions for where to look next would be most appreciated.