Compalitation errors when running stanc and stan_model on Windows

Summary:

Can't build stan model using stanc and stan_model

Reproducible Steps:

library(rstan)
fixed_effect <- 
"data {
  int<lower=1> N; //number of data points
  int<lower=1> K;
  real intensity[N]; //protein or peptide intensity
  matrix[N,K] dilution;  //design matrix (predictor)
}

parameters {
  vector[K] beta;            //intercept and slope
  real<lower=0> sigma_e;     //error sd
}

model {
  intensity ~ normal(dilution * beta , sigma_e);
}
"

rt <- stanc(model_code = fixed_effect)
sm <- stan_model(stanc_ret = rt, verbose = FALSE)

Current Output:

> sm <- stan_model(stanc_ret = rt, verbose = FALSE)
make cmd is
  make -f "C:/PROGRA~1/R/R-40~1.3/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-40~1.3/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file9746d052a95.dll" WIN=64 TCLBIN=64 OBJECTS="file9746d052a95.o"

make would use
if test "zfile9746d052a95.o" != "z"; then \
  if test -e "file9746d052a95-win.def"; then \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file9746d052a95.dll file9746d052a95-win.def file9746d052a95.o   "C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file9746d052a95.dll file9746d052a95-win.def file9746d052a95.o   "C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
  else \
    echo EXPORTS > tmp.def; \
    "C:/rtools40/mingw64/bin/"nm file9746d052a95.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 file9746d052a95.dll tmp.def file9746d052a95.o   "C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file9746d052a95.dll tmp.def file9746d052a95.o   "C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi
Error in compileCode(f, code, language = language, verbose = verbose) : 
  C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.data$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::P1'; file9746d052a95.o:file9746d052a95.cpp:(.rdata$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): first defined hereC:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.data$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QS[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QS]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::QS'; file9746d052a95.o
Error in sink(type = "output") : invalid connection

RStan Version:

packageVersion("rstan")
[1] ‘2.21.2’

R Version:

The version of R you are running (e.g., from R.version.string)

> R.version.string
[1] "R version 4.0.3 (2020-10-10)"

Operating System:

Windows 10.

Start by reproducing the stanc() and stan_model() calls from the issue with rstan 2.21.2 on R 4.0.3 and Windows 10. Inspect the compileCode linker output, including the generated file9746d052a95.cpp and libStanServices.a, to determine the source of the duplicate Boost symbols. Done means the supplied model compiles successfully on the reported Windows setup without the multiple-definition error.