Hi all,
I am pretty new with Stan. However, in the past months I have been able to run, without too many problems, various models. Recently, I have added a new model:
modelFitRef_LM <- stan(
file = "deltaRuleLinearModel.stan", # Stan program; make sure this is in the same directory you have declared at the top of this script.
data = allDataStan, # named list of data
chains = 4, # number of Markov chains
warmup = 2000, # number of warmup iterations per chain
iter = 4000, # total number of iterations per chain
cores = 4, # number of cores (could use one per chain)
refresh = 0 # no progress shown
)
which is a very similar model to others that have presented no issue at all in running. In addition, colleagues of mine did not have any problems in running this script so I believe it is something wrong with my machine.
This is the error message that I receive:
Warning in system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
'C:/rtools40/usr/mingw_/bin/g++' not found
make cmd is
make -f "C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-40~1.2/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file16907b108d9.dll" WIN=64 TCLBIN=64 OBJECTS="file16907b108d9.o"
make would use
"C:/rtools40/mingw64/bin/"g++ -std=gnu++14 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/Rcpp/include/" -I"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/RcppEigen/include/" -I"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/RcppEigen/include/unsupported" -I"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/BH/include" -I"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/StanHeaders/include/src/" -I"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/StanHeaders/include/" -I"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/RcppParallel/include/" -I"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include "C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp" -std=c++1y -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c file16907b108d9.cpp -o file16907b108d9.o
if test "zfile16907b108d9.o" != "z"; then \
if test -e "file16907b108d9-win.def"; then \
echo "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file16907b108d9.dll file16907b108d9-win.def file16907b108d9.o "C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.2/bin/x64" -lR ; \
"C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file16907b108d9.dll file16907b108d9-win.def file16907b108d9.o "C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.2/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
"C:/rtools40/mingw64/bin/"nm file16907b108d9.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 file16907b108d9.dll tmp.def file16907b108d9.o "C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.2/bin/x64" -lR ; \
"C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file16907b108d9.dll tmp.def file16907b108d9.o "C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.2/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
Error in compileCode(f, code, language = language, verbose = verbose) :
from file16907b108d9.cpp:14:C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope:C:/Users/ic18563/OneDrive - University of Bristol/Documents/R/win-library/4.0/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-40~1.2/etc/x64/Makeconf:229: file16907b108d9.o] Error 1
Error in sink(type = "output") : invalid connection
I have tried all the suggestions recommended in the forum without any success in solving the issue.
I am using this R version:
RStudio Version 1.4.1717
and this Stan version:
packageVersion("rstan")
[1] ‘2.21.2’
and I am working with Windows 10 Enterprise.
Please any suggestion is welcome! I have tried now to solve this problem for a while and without any success.
Many thanks in advance for your help!