Compilation error on Rstan

Interfaces RStan
1

Have to work with lots of error on Stan, this is what I got when compiling. Please help me to solve this:

**Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: In system(cmd, intern = !verbose) :
  running command 'C:/PROGRA~1/R/R-40~1.2/bin/x64/R CMD SHLIB file2aa871844643.cpp 2> file2aa871844643.cpp.err.txt' had status 1
2: In file(con, "r") :
  cannot open file 'file2aa871844643.cpp.err.txt': No such file or directory
Error in sink(type = "output") : invalid connection**

If possible, add also code to simulate data or attach a (subset of) the dataset you work with.

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2

We need to see the output of

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

particularly the part under the line that says “Compilation argument”.

3

It gives me a long output. Last few lines of it:

SAMPLING FOR MODEL ‘73fc79f8b1915e8208c736914c86d1a1’ NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: Iteration: 1 / 2000 [ 0%] (Warmup)
Chain 4: Iteration: 200 / 2000 [ 10%] (Warmup)
Chain 4: Iteration: 400 / 2000 [ 20%] (Warmup)
Chain 4: Iteration: 600 / 2000 [ 30%] (Warmup)
Chain 4: Iteration: 800 / 2000 [ 40%] (Warmup)
Chain 4: Iteration: 1000 / 2000 [ 50%] (Warmup)
Chain 4: Iteration: 1001 / 2000 [ 50%] (Sampling)
Chain 4: Iteration: 1200 / 2000 [ 60%] (Sampling)
Chain 4: Iteration: 1400 / 2000 [ 70%] (Sampling)
Chain 4: Iteration: 1600 / 2000 [ 80%] (Sampling)
Chain 4: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 4: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.011 seconds (Warm-up)
Chain 4: 0.014 seconds (Sampling)
Chain 4: 0.025 seconds (Total)
Chain 4:

After that, I complied my program again, but having the same error as earlier.

Error in file(con, “r”) : cannot open the connection
In addition: Warning messages:
1: In system(cmd, intern = !verbose) :
running command ‘C:/PROGRA~1/R/R-40~1.2/bin/x64/R CMD SHLIB file2c587e151aa4.cpp 2> file2c587e151aa4.cpp.err.txt’ had status 1
2: In file(con, “r”) :
cannot open file ‘file2c587e151aa4.cpp.err.txt’: No such file or directory
Error in sink(type = “output”) : invalid connection

Would like to know that why is this?

4

You you try your program but passing verbose = TRUE when you call stan or sampling?

5

Do you mean run like this?
stan(model_code=model, data= data_list, warmup = 500,
iter = 1000, chains = 2,verbose = TRUE)

6

Yes

7

Then, this error noticed,

Error in file(con, “r”) : cannot open the connection
In addition: Warning message:
In file(con, “r”) :
cannot open file ‘file2c581a232c8d.cpp.err.txt’: No such file or directory

8

There should be a lot more. Specifically, we are looking for the paragraphs following the line that says “Compilation argument”.

9

I think it would be an error of my model block.

10

Hi, I tried it in different ways, but failed,

Compilation argument:
C:/PROGRA~1/R/R-40~1.2/bin/x64/R CMD SHLIB file2c5813821819.cpp 2> file2c5813821819.cpp.err.txt

11

What is the part after the “Compilation argument” line? It should be similar to

Compilation argument: /home/ben/r-devel/bin/R CMD SHLIB file4a1a333174a.cpp 2> file4a1a333174a.cpp.err.txt g++-8 -std=gnu++14 -I"/home/ben/r-devel/include" -DNDEBUG -I"/home/ben/r-devel/library/Rcpp/include/" -I"/home/ben/r-devel/library/RcppEigen/include/" -I"/home/ben/r-devel/library/RcppEigen/include/unsupported" -I"/home/ben/r-devel/library/BH/include" -I"/home/ben/r-devel/library/StanHeaders/include/src/" -I"/home/ben/r-devel/library/StanHeaders/include/" -I"/home/ben/r-devel/library/RcppParallel/include/" -I"/home/ben/r-devel/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/home/ben/r-devel/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fpic -O3 -g0 -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-unknown-pragmas -c file4a1a333174a.cpp -o file4a1a333174a.o

12

Like this,
Compilation argument:
C:/PROGRA~1/R/R-40~1.2/bin/x64/R CMD SHLIB file2c5817d021ca.cpp 2> file2c5817d021ca.cpp.err.txt
“C:/rtools40/mingw64/bin/“g++ -std=gnu++14 -I"C:/PROGRA~1/R/R-40~1.2/include” -DNDEBUG -I"C:/Users/erandi/Documents/R/win-library/4.0/Rcpp/include/” -I"C:/Users/erandi/Documents/R/win-library/4.0/RcppEigen/include/" -I"C:/Users/erandi/Documents/R/win-library/4.0/RcppEigen/include/unsupported" -I"C:/Users/erandi/Documents/R/win-library/4.0/BH/include" -I"C:/Users/erandi/Documents/R/win-library/4.0/StanHeaders/include/src/" -I"C:/Users/erandi/Documents/R/win-library/4.0/StanHeaders/include/" -I"C:/Users/erandi/Documents/R/win-library/4.0/rstan/include" -DEIGEN_NO_DEBUG -D_REENTRANT -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -include stan/math/prim/mat/fun/Eigen.hpp -std=c++1y -march=core2 -include C:/Users/erandi/Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp -I “C:/Users/erandi/Documents/R/win-library/4.0/StanHeaders/include” -I “C:/Users/erandi/Documents/R/win-library/4.0/RcppEigen/include” -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c file2c5817d021ca.cpp -o file2c5817d021ca.o
file2c5817d021ca.cpp:6:36: warning: ISO C++11 requires whitespace after the macro name
#define STAN__SERVICES__COMMAND_HPP#include <boost/integer/integer_log2.hpp>

13

Do you have any idea about

file2c585b18381.cpp:375:1452: note: cannot convert ‘stan::math::array_builder::array() with T = stan::math::var’ (type ‘std::vectorstan::math::var’) to type ‘const std::vector&’

This is a part of error what I got earlier.