Trouble replicating a journal article on firearm mortality in rstan

General
1

I’m new to rstan and been trying to replicate the results from a recently published journal article that used rstan to do some Bayesian modeling. (Replication code available here.) I have followed the installation instructions posted here, but am running into the following error when I try to run the model.

# total iterations per chain.
iter = 1000

# fit the model via MCMC
M <- stan(file = "C:/Users/mvbondy/Dropbox (Stanford Law School)/Team_Donohue/RTC (New)/misc requests/PNAS_Paper/NegBinFinal.stan",
                            data = stan.data ,
                            pars = c("alpha","betachI","betach6","betaI","beta6","delta", "gamma","zeta","invphi"),
                            iter=iter)

That results in the following output

make cmd is
  make -f "C:/PROGRA~1/R/R-41~1.1/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-41~1.1/share/make/winshlib.mk" -f "C:/Users/mvbondy/Documents/.R/Makevars.win" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file28c07b815915.dll" WIN=64 TCLBIN=64 OBJECTS="file28c07b815915.o"

make would use
"C:/rtools40/mingw64/bin/"g++  -std=gnu++14 -I"C:/PROGRA~1/R/R-41~1.1/include" -DNDEBUG   -I"C:/Users/mvbondy/Documents/R/win-library/4.1/Rcpp/include/"  -I"C:/Users/mvbondy/Documents/R/win-library/4.1/RcppEigen/include/"  -I"C:/Users/mvbondy/Documents/R/win-library/4.1/RcppEigen/include/unsupported"  -I"C:/Users/mvbondy/Documents/R/win-library/4.1/BH/include" -I"C:/Users/mvbondy/Documents/R/win-library/4.1/StanHeaders/include/src/"  -I"C:/Users/mvbondy/Documents/R/win-library/4.1/StanHeaders/include/"  -I"C:/Users/mvbondy/Documents/R/win-library/4.1/RcppParallel/include/"  -I"C:/Users/mvbondy/Documents/R/win-library/4.1/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DBOOST_NO_AUTO_PTR  -include "C:/Users/mvbondy/Documents/R/win-library/4.1/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp"  -std=c++1y         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -mtune=native -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -c file28c07b815915.cpp -o file28c07b815915.o
if test "zfile28c07b815915.o" != "z"; then \
  if test -e "file28c07b815915-win.def"; then \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file28c07b815915.dll file28c07b815915-win.def file28c07b815915.o   "C:/Users/mvbondy/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/mvbondy/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/mvbondy/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-41~1.1/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file28c07b815915.dll file28c07b815915-win.def file28c07b815915.o   "C:/Users/mvbondy/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/mvbondy/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/mvbondy/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-41~1.1/bin/x64" -lR ; \
  else \
    echo EXPORTS > tmp.def; \
    "C:/rtools40/mingw64/bin/"nm file28c07b815915.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g'  >> tmp.def; \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file28c07b815915.dll tmp.def file28c07b815915.o   "C:/Users/mvbondy/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/mvbondy/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/mvbondy/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-41~1.1/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file28c07b815915.dll tmp.def file28c07b815915.o   "C:/Users/mvbondy/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/mvbondy/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/mvbondy/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-41~1.1/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi
Error in compileCode(f, code, language = language, verbose = verbose) : 
                   from file28c07b815915.cpp:14:C:/Users/mvbondy/Documents/R/win-library/4.1/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope:C:/Users/mvbondy/Documents/R/win-library/4.1/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: 'void stan::math::set_zero_all_adjoints()' defined but not used [-Wunused-function] static void set_zero_all_adjoints() {             ^~~~~~~~~~~~~~~~~~~~~make: *** [C:/PROGRA~1/R/R-41~1.1/etc/x64/Makeconf:245: file28c07b815915.o] Error 1
In addition: Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/rtools40/usr/mingw_/bin/g++' not found
Error in sink(type = "output") : invalid connection

I was hoping this is a simple software installation problem and someone could help point me in the right direction. Much appreciated.

2

Searching the internet for the symptom

Error in sink(type = "output") : invalid connection

finds a few earlier discussions of similar windows build issues with some suggested fixes:

2 Likes
3

Can you try installing the preview of the next rstan version and running again:

remove.packages(c("StanHeaders", "rstan"))
install.packages("StanHeaders", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
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