##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL STAN
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library’
* installing *source* package ‘STAN’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c Bernoulli.cpp -o Bernoulli.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c EmissionFactory.cpp -o EmissionFactory.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c EmissionFunction.cpp -o EmissionFunction.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/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 arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c InitialProbability.cpp -o InitialProbability.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c JointlyIndependent.cpp -o JointlyIndependent.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c MemoryAllocation.cpp -o MemoryAllocation.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c Multinomial.cpp -o Multinomial.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c MultivariateGaussian.cpp -o MultivariateGaussian.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c NegativeBinomial.cpp -o NegativeBinomial.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c Poisson.cpp -o Poisson.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c PoissonLogNormal.cpp -o PoissonLogNormal.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c RAccessUtils.cpp -o RAccessUtils.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/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 arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c TransitionMatrix.cpp -o TransitionMatrix.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -D_RDLL_   -fPIC  -falign-functions=64 -Wall -g -O2  -c matUtils.cpp -o matUtils.o
matUtils.cpp:114:10: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    for (register int i = 0 ; i < myN ; i++)
         ^~~~~~~~~
matUtils.cpp:115:14: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
        for (register int j = i ; j < myldz ; j++)
             ^~~~~~~~~
matUtils.cpp:125:10: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    for (register int i = 0 ; i < myNCol ; i++)
         ^~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o STAN.so Bernoulli.o EmissionFactory.o EmissionFunction.o HMM.o InitialProbability.o JointlyIndependent.o MemoryAllocation.o Multinomial.o MultivariateGaussian.o NegativeBinomial.o ParamContainerEmissions.o Poisson.o PoissonLogNormal.o RAccessUtils.o RWrapper.o TransitionMatrix.o matUtils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-STAN/00new/STAN/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (STAN)