############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL STAN ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'STAN' ... ** using staged installation ** libs g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Bernoulli.cpp -o Bernoulli.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c EmissionFactory.cpp -o EmissionFactory.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c EmissionFunction.cpp -o EmissionFunction.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c HMM.cpp -o HMM.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c InitialProbability.cpp -o InitialProbability.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c JointlyIndependent.cpp -o JointlyIndependent.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MemoryAllocation.cpp -o MemoryAllocation.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Multinomial.cpp -o Multinomial.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MultivariateGaussian.cpp -o MultivariateGaussian.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NegativeBinomial.cpp -o NegativeBinomial.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Poisson.cpp -o Poisson.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PoissonLogNormal.cpp -o PoissonLogNormal.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RAccessUtils.cpp -o RAccessUtils.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] 350 | 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] 1157 | return sexpemissionParam; | ^~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TransitionMatrix.cpp -o TransitionMatrix.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matUtils.cpp -o matUtils.o g++ -std=gnu++14 -shared -s -static-libgcc -o STAN.dll tmp.def 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 -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-STAN/00new/STAN/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (STAN)