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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL STAN
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘STAN’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c Bernoulli.cpp -o Bernoulli.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c EmissionFactory.cpp -o EmissionFactory.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c EmissionFunction.cpp -o EmissionFunction.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c HMM.cpp -o HMM.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c InitialProbability.cpp -o InitialProbability.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c JointlyIndependent.cpp -o JointlyIndependent.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c MemoryAllocation.cpp -o MemoryAllocation.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c Multinomial.cpp -o Multinomial.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c MultivariateGaussian.cpp -o MultivariateGaussian.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c NegativeBinomial.cpp -o NegativeBinomial.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c Poisson.cpp -o Poisson.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c PoissonLogNormal.cpp -o PoissonLogNormal.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c RAccessUtils.cpp -o RAccessUtils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c RWrapper.cpp -o RWrapper.o
RWrapper.cpp: In function ‘EmissionFunction** RGETEMISSION(SEXP, int, SEXP, int*, const char*, double***, int*, int, SEXP, int*, int*, int*)’:
RWrapper.cpp:350:16: warning: ‘HMMEmissionFunctions’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         return HMMEmissionFunctions;
                ^~~~~~~~~~~~~~~~~~~~
RWrapper.cpp: In function ‘SEXPREC* prepareEmission(const char*, SEXP, SEXP, EmissionFunction**, int)’:
RWrapper.cpp:1157:16: warning: ‘sexpemissionParam’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         return sexpemissionParam;
                ^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c TransitionMatrix.cpp -o TransitionMatrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c matUtils.cpp -o matUtils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/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/home/biocbuild/bbs-3.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/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)