Package building with rstantools 2.0.0

asael_am · September 24, 2019, 11:50pm

Hi everyone I am curremtly trying to build my package following the process in vignette but when I run the option:

pkgbuild::compile_dll()

I get the next error:
C:/Users/asael/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/meta/is_constant.hpp:27:39: error: expected primary-expression before ‘,’ token
enum { value = std::is_convertible<T, double>::value };
^
C:/Users/asael/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/meta/is_constant.hpp:27:41: error: expected identifier before ‘double’
enum { value = std::is_convertible<T, double>::value };
^
C:/Users/asael/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/meta/is_constant.hpp:27:41: error: expected ‘}’ before ‘double’
C:/Users/asael/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/meta/is_constant.hpp:27:47: error: expected unqualified-id before ‘>’ token
enum { value = std::is_convertible<T, double>::value };
^
C:/Users/asael/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/meta/is_constant.hpp:30:1: error: expected declaration before ‘}’ token
} // namespace stan
^
make: *** [C:/PROGRA~1/R/R-36~1.1/etc/x64/Makeconf:213: stanExports_NVarBekk.o] Error 1
ERROR: compilation failed for package ‘varstan’

removing ‘C:/Users/asael/AppData/Local/Temp/RtmpMRBfkL/devtools_install_3954150845bd/varstan’
Error in (function (command = NULL, args = character(), error_on_status = TRUE, :
System command error

And dont know how to solve it. Thanks for the help

bgoodri · September 25, 2019, 1:19am

Most likely a C++14 thing. Make sure you have this configuration for building source packages related to RStan

jonah · September 25, 2019, 1:34am

@bgoodri is there a way we can add something in rstantools to check for that config and avoid the confusing error that @asael_am had?

bgoodri · September 25, 2019, 1:46am

I think we would have to do something like

Sys.setenv(CXX14 = 1)
Rcpp::evalCpp("__cplusplus >= 201402L")

asael_am · September 25, 2019, 3:04am

@bgoodri @jonah I already have that config that I did when I install rstan for the first time.

Now when I run:
rstan_create_package(“foo_packg”)

In the src carpet rstantools creates makevar and makevars.win default files

And I put the config you recomend on it but doesnt work either way. Throws the same error

bgoodri · September 25, 2019, 3:51am

Maybe do

Sys.setenv(USE_CXX14 = 1)

before doing

pkgbuild::compile_dll()

?

asael_am · September 25, 2019, 4:00am

Now I got this error:

g++ -m64 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.1/include" -DNDEBUG -I"…/inst/include" -I"C:/Users/asael/Documents/R/win-library/3.6/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I"C:/Users/asael/Documents/R/win-library/3.6/BH/include" -I"C:/Users/asael/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/asael/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/asael/Documents/R/win-library/3.6/rstan/include" -I"C:/Users/asael/Documents/R/win-library/3.6/StanHeaders/include" -O3 -march=native -c RcppExports.cpp -o RcppExports.o
sh: g++: command not found
make: *** [C:/PROGRA~1/R/R-36~1.1/etc/x64/Makeconf:215: RcppExports.o] Error 127
ERROR: compilation failed for package ‘varstan’

removing ‘C:/Users/asael/AppData/Local/Temp/Rtmp02QNVL/devtools_install_708259d180b/varstan’
Error in (function (command = NULL, args = character(), error_on_status = TRUE, :
System command error

When I run
pkgbuild::compile_dll()

The Makevars file in src returns to its default code

bgoodri · September 25, 2019, 4:43am

What does

pkgbuild::has_build_tools(debug = TRUE)

say?

asael_am · September 25, 2019, 11:26am

It says this:

pkgbuild::has_build_tools(debug = TRUE)
[1] TRUE

jonah · September 25, 2019, 7:58pm

@bgoodri Any other ideas? Is it possibly not a C++14 issue?

@asael_am Sorry it’s still not working. Does this happen if you create the demo rstanlm package from the vignette (I presume it does) or just with your package? Also, can you compile Stan programs in general just not in the package? Or is this happening with you compile regular Stan programs too?

asael_am · September 25, 2019, 8:04pm

I DONT KNOW It says that doesnt found the g++ file: And every time I ran it the makevars files became the deffault ones.

I even try with the linear model example in the vignettes and follow the code there, but doesnt work :(

Charles_Driver · September 25, 2019, 8:25pm

I / users of my software regularly face this problem. The advice that rtools does not need to be in the system path doesn’t seem appropriate sometimes. The ctsem github page describes some changes that should resolve the issue, assuming rtools is installed in c:\Rtools
A better solution would be wonderful, not sure what is going wrong though.

asael_am · September 25, 2019, 8:28pm

Ok nice but I dont understand you sorry, this is my first try building an R package using stan

bgoodri · September 25, 2019, 10:18pm

Possibly

pkgbuild::with_build_tools(pkgbuild::compile_dll())

?

asael_am · September 26, 2019, 12:34am

Still having this error:

g++ -m64 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.1/include" -DNDEBUG -I"…/inst/include" -I"C:/Users/asael/Documents/R/win-library/3.6/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I"C:/Users/asael/Documents/R/win-library/3.6/BH/include" -I"C:/Users/asael/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/asael/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/asael/Documents/R/win-library/3.6/rstan/include" -I"C:/Users/asael/Documents/R/win-library/3.6/StanHeaders/include" -O3 -march=native -c RcppExports.cpp -o RcppExports.o
sh: g++: command not found
make: *** [C:/PROGRA~1/R/R-36~1.1/etc/x64/Makeconf:215: RcppExports.o] Error 127
ERROR: compilation failed for package ‘varstan’

removing ‘C:/Users/asael/AppData/Local/Temp/RtmpkNVqs4/devtools_install_25d875c0f57/varstan’
Error in (function (command = NULL, args = character(), error_on_status = TRUE, :
System command error

:( :(

asael_am · September 26, 2019, 12:44am

I cannot run the demo rstanlm package! A I can run stan programs I actually run my package functions with the precompiled models simulating the package dynamics and everything works fine, the problem is when I try to build the package itself

asael_am · September 26, 2019, 12:58am

I follow what you use in the ctsem package:

Put my stan files in the folder stan_files inside src
Change my makevar and makevar.win
Copy your tools folder with the make_cc file
Abd ran again:
The error is:

“C:/PROGRA~1/R/R-36~1.1/bin/x64/Rscript” -e “source(file.path(’…’, ‘tools’, ‘make_cc.R’)); make_cc(commandArgs(TRUE))” stan_files/NVarBekk.stan
Wrote C++ file “stan_files/NVarBekk.cc”
g++ -m64 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.1/include" -DNDEBUG -I"…/inst/include" -I"C:/Users/asael/Documents/R/win-library/3.6/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"C:/Users/asael/Documents/R/win-library/3.6/BH/include" -I"C:/Users/asael/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/asael/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/asael/Documents/R/win-library/3.6/rstan/include" -I"C:/Users/asael/Documents/R/win-library/3.6/StanHeaders/include" -O3 -march=native -c stan_files/NVarBekk.cc -o stan_files/NVarBekk.o
sh: g++: command not found
make: *** [C:/PROGRA~1/R/R-36~1.1/etc/x64/Makeconf:213: stan_files/NVarBekk.o] Error 127
rm stan_files/NVarBekk.cc
ERROR: compilation failed for package ‘varstan’

removing ‘C:/Users/asael/AppData/Local/Temp/RtmpkNVqs4/devtools_install_25d8541b6ff0/varstan’
Error in (function (command = NULL, args = character(), error_on_status = TRUE, :
System command error

bgoodri · September 26, 2019, 1:56am

Can you compile your package outside RStudio?

asael_am · September 26, 2019, 2:00am

I dont know how to do that!

Do you know where I can read about it?

asael_am · September 26, 2019, 2:05am

@bgoodri @jonah I think the real problem is here:

g++: command not found
But I dont know what it means