############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL STAN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘STAN’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c Bernoulli.cpp -o Bernoulli.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c EmissionFactory.cpp -o EmissionFactory.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c EmissionFunction.cpp -o EmissionFunction.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c HMM.cpp -o HMM.o HMM.cpp:967:12: warning: variable 'allT' set but not used [-Wunused-but-set-variable] double allT = 0; ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c InitialProbability.cpp -o InitialProbability.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c JointlyIndependent.cpp -o JointlyIndependent.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c MemoryAllocation.cpp -o MemoryAllocation.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c Multinomial.cpp -o Multinomial.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c MultivariateGaussian.cpp -o MultivariateGaussian.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c NegativeBinomial.cpp -o NegativeBinomial.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c Poisson.cpp -o Poisson.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c PoissonLogNormal.cpp -o PoissonLogNormal.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c RAccessUtils.cpp -o RAccessUtils.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c RWrapper.cpp -o RWrapper.o RWrapper.cpp:343:17: warning: variable 'HMMEmissionFunctions' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if(strcmp(type,poissonlognormal) == 0) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RWrapper.cpp:350:16: note: uninitialized use occurs here return HMMEmissionFunctions; ^~~~~~~~~~~~~~~~~~~~ RWrapper.cpp:343:14: note: remove the 'if' if its condition is always true else if(strcmp(type,poissonlognormal) == 0) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RWrapper.cpp:311:48: note: initialize the variable 'HMMEmissionFunctions' to silence this warning EmissionFunction **HMMEmissionFunctions; ^ = nullptr RWrapper.cpp:1140:21: warning: variable 'sexpemissionParam' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if(strcmp(type, multinomial) == 0) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RWrapper.cpp:1157:16: note: uninitialized use occurs here return sexpemissionParam; ^~~~~~~~~~~~~~~~~ RWrapper.cpp:1140:18: note: remove the 'if' if its condition is always true else if(strcmp(type, multinomial) == 0) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RWrapper.cpp:1123:31: note: initialize the variable 'sexpemissionParam' to silence this warning SEXP sexpemissionParam; ^ = nullptr 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c TransitionMatrix.cpp -o TransitionMatrix.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c matUtils.cpp -o matUtils.o matUtils.cpp:114:10: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] for (register int i = 0 ; i < myN ; i++) ^~~~~~~~~ matUtils.cpp:115:14: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] for (register int j = i ; j < myldz ; j++) ^~~~~~~~~ matUtils.cpp:118:5: error: no matching function for call to 'dspev_' F77_NAME(dspev)("V", "U", &myN, myAP, myW, myZ, &myldz, myWork, &myInfo) ; ^~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:81:24: note: expanded from macro 'F77_NAME' #define F77_NAME(x) F77_CALL(x) ^~~~~~~~~~~ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:77:22: note: expanded from macro 'F77_CALL' # define F77_CALL(x) x ## _ ^~~~~~ :337:1: note: expanded from here dspev_ ^~~~~~ /Library/Frameworks/R.framework/Resources/include/R_ext/Lapack.h:1050:1: note: candidate function not viable: requires 11 arguments, but 9 were provided F77_NAME(dspev)(const char* jobz, const char* uplo, const int* n, ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:81:24: note: expanded from macro 'F77_NAME' #define F77_NAME(x) F77_CALL(x) ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:77:22: note: expanded from macro 'F77_CALL' # define F77_CALL(x) x ## _ ^ :43:1: note: expanded from here dspev_ ^ matUtils.cpp:125:10: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] for (register int i = 0 ; i < myNCol ; i++) ^~~~~~~~~ 4 errors generated. make: *** [matUtils.o] Error 1 ERROR: compilation failed for package ‘STAN’ * removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/STAN’