############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/STAN_2.20.0.tar.gz && rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=STAN.buildbin-libdir STAN_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL STAN_2.20.0.zip && rm STAN_2.20.0.tar.gz STAN_2.20.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 293k 100 293k 0 0 1115k 0 --:--:-- --:--:-- --:--:-- 1119k install for i386 * installing *source* package 'STAN' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Bernoulli.cpp -o Bernoulli.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c EmissionFactory.cpp -o EmissionFactory.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c EmissionFunction.cpp -o EmissionFunction.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c HMM.cpp -o HMM.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c InitialProbability.cpp -o InitialProbability.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c JointlyIndependent.cpp -o JointlyIndependent.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MemoryAllocation.cpp -o MemoryAllocation.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Multinomial.cpp -o Multinomial.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MultivariateGaussian.cpp -o MultivariateGaussian.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NegativeBinomial.cpp -o NegativeBinomial.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Poisson.cpp -o Poisson.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PoissonLogNormal.cpp -o PoissonLogNormal.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RAccessUtils.cpp -o RAccessUtils.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/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] 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; ^~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TransitionMatrix.cpp -o TransitionMatrix.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matUtils.cpp -o matUtils.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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 -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -fopenmp -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/STAN.buildbin-libdir/00LOCK-STAN/00new/STAN/libs/i386 ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'STAN' finding HTML links ... done DimNames html DirScore html Emission html EmissionParams html HMM-class html HMM html HMMEmission-class html HMMEmission html InitProb html LogLik html STAN-package html StateNames html Transitions html bdHMM-class html bdHMM html binarizeData html c2optimize html call_dpoilog html data2Gviz html example html fitBdClust html fitHMM html flags html getAvgSignal html getLogLik html getPosterior html getSizeFactors html getViterbi html initBdClust html initBdHMM html initHMM html observations html pilot.hg19 html runningMean html sub-HMM-ANY-ANY-ANY-method html sub-bdHMM-ANY-ANY-ANY-method html trainRegions html ucscGenes html viterbi2GRanges html viterbi2Gviz html yeastTF_SGDGenes html yeastTF_databychrom_ex html ** 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 install for x64 * installing *source* package 'STAN' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Bernoulli.cpp -o Bernoulli.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c EmissionFactory.cpp -o EmissionFactory.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c EmissionFunction.cpp -o EmissionFunction.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c HMM.cpp -o HMM.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c InitialProbability.cpp -o InitialProbability.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c JointlyIndependent.cpp -o JointlyIndependent.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MemoryAllocation.cpp -o MemoryAllocation.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Multinomial.cpp -o Multinomial.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MultivariateGaussian.cpp -o MultivariateGaussian.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NegativeBinomial.cpp -o NegativeBinomial.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Poisson.cpp -o Poisson.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PoissonLogNormal.cpp -o PoissonLogNormal.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RAccessUtils.cpp -o RAccessUtils.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/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] 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; ^~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TransitionMatrix.cpp -o TransitionMatrix.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matUtils.cpp -o matUtils.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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 -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/STAN.buildbin-libdir/STAN/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'STAN' as STAN_2.20.0.zip * DONE (STAN) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'STAN' successfully unpacked and MD5 sums checked