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###
### Running command:
###
### chmod a+r STAN -R && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data STAN
###
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* checking for file 'STAN/DESCRIPTION' ... OK
* preparing 'STAN':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
Warning: running command '"C:/Users/biocbuild/bbs-3.6-bioc/R/bin/x64/Rcmd.exe" INSTALL -l "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpWSeBCR\Rinst1e7053bd135b" --no-multiarch "C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWSeBCR/Rbuild1e702226664f/STAN"' had status 1
-----------------------------------
* installing *source* package 'STAN' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c Bernoulli.cpp -o Bernoulli.o
Bernoulli.cpp: In constructor 'Bernoulli::Bernoulli(ParamContainerEmissions*)':
Bernoulli.cpp:25:13: warning: unused variable 'd2' [-Wunused-variable]
int d1, d2;
^
Bernoulli.cpp: In destructor 'virtual Bernoulli::˜Bernoulli()':
Bernoulli.cpp:37:9: warning: unused variable 'd1' [-Wunused-variable]
int d1;
^
Bernoulli.cpp: In member function 'virtual double Bernoulli::calcEmissionProbability(double*, int, int)':
Bernoulli.cpp:60:12: warning: unused variable 'j' [-Wunused-variable]
int i, j, obs_i;
^
Bernoulli.cpp: In member function 'virtual void Bernoulli::updateAuxiliaries(double***, double**, double*, int*, int, int, int**)':
Bernoulli.cpp:99:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
Bernoulli.cpp: In member function 'virtual void Bernoulli::updateAuxiliariesCoupled(double***, double**, double*, int*, int, int, int, int**)':
Bernoulli.cpp:140:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
Bernoulli.cpp: In member function 'virtual void Bernoulli::updateAuxiliariesCoupledRevop(double***, double**, double*, int*, int, int, int, int*, int*, int**)':
Bernoulli.cpp:170:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
Bernoulli.cpp: In member function 'virtual void Bernoulli::updateCoupledRevop(double***, double*, int, int*, int*, double**, int**, SEXP, int, int)':
Bernoulli.cpp:218:9: warning: unused variable 'skipcounter' [-Wunused-variable]
int skipcounter = 0;
^
Bernoulli.cpp: In member function 'virtual void Bernoulli::update(double***, double*, int**, SEXP, int, int)':
Bernoulli.cpp:262:9: warning: unused variable 'skipcounter' [-Wunused-variable]
int skipcounter = 0;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c EmissionFactory.cpp -o EmissionFactory.o
In file included from EmissionFactory.cpp:1:0:
EmissionFactory.h: In member function 'virtual EmissionFunction* EmissionFactory::createEmissionFunctionMixed(std::list<EmissionFunction*>, ParamContainerEmissions*)':
EmissionFactory.h:17:133: warning: no return statement in function returning non-void [-Wreturn-type]
virtual EmissionFunction* createEmissionFunctionMixed(list<EmissionFunction*> efb, ParamContainerEmissions *emissionParams){};
^
In file included from EmissionFactory.cpp:8:0:
JointlyIndependentFactory.h: In member function 'virtual EmissionFunction* JointlyIndependentFactory::createEmissionFunctionMixed(std::list<EmissionFunction*>, ParamContainerEmissions*)':
JointlyIndependentFactory.h:28:17: warning: unused variable 'parallel' [-Wunused-variable]
int parallel=0;
^
In file included from EmissionFactory.cpp:2:0:
MultivariateGaussianFactory.h: In member function 'virtual EmissionFunction* MultivariateGaussianFactory::createEmissionFunction(ParamContainerEmissions*, int)':
MultivariateGaussianFactory.h:23:9: warning: control reaches end of non-void function [-Wreturn-type]
}
^
In file included from EmissionFactory.cpp:3:0:
BernoulliFactory.h: In member function 'virtual EmissionFunction* BernoulliFactory::createEmissionFunction(ParamContainerEmissions*, int)':
BernoulliFactory.h:27:9: warning: control reaches end of non-void function [-Wreturn-type]
}
^
In file included from EmissionFactory.cpp:4:0:
PoissonFactory.h: In member function 'virtual EmissionFunction* PoissonFactory::createEmissionFunction(ParamContainerEmissions*, int)':
PoissonFactory.h:24:9: warning: control reaches end of non-void function [-Wreturn-type]
}
^
In file included from EmissionFactory.cpp:5:0:
MultinomialFactory.h: In member function 'virtual EmissionFunction* MultinomialFactory::createEmissionFunction(ParamContainerEmissions*, int)':
MultinomialFactory.h:24:9: warning: control reaches end of non-void function [-Wreturn-type]
}
^
In file included from EmissionFactory.cpp:6:0:
NegativeBinomialFactory.h: In member function 'virtual EmissionFunction* NegativeBinomialFactory::createEmissionFunction(ParamContainerEmissions*, int)':
NegativeBinomialFactory.h:27:9: warning: control reaches end of non-void function [-Wreturn-type]
}
^
In file included from EmissionFactory.cpp:7:0:
PoissonLogNormalFactory.h: In member function 'virtual EmissionFunction* PoissonLogNormalFactory::createEmissionFunction(ParamContainerEmissions*, int)':
PoissonLogNormalFactory.h:27:9: warning: control reaches end of non-void function [-Wreturn-type]
}
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c EmissionFunction.cpp -o EmissionFunction.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c HMM.cpp -o HMM.o
HMM.cpp: In member function 'virtual void HMM::calcEmissionProbs(double***, double**, int*, int, int**, int*, int*, int**, int, int, int*)':
HMM.cpp:112:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,t,k;
^
HMM.cpp:112:19: warning: unused variable 'k' [-Wunused-variable]
int i,j,t,k;
^
HMM.cpp:113:16: warning: unused variable 'denom' [-Wunused-variable]
double denom;
^
HMM.cpp:57:12: warning: unused variable 'proba' [-Wunused-variable]
double proba;
^
HMM.cpp:105:14: warning: unused variable 'myTransMat' [-Wunused-variable]
double **myTransMat = this->A->getTransMat();
^
HMM.cpp: In member function 'void HMM::getGamma(double**, double**, double*, double**, double**, int*, int, int, double, int)':
HMM.cpp:400:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,t,k;
^
HMM.cpp:400:19: warning: unused variable 'k' [-Wunused-variable]
int i,j,t,k;
^
HMM.cpp:395:14: warning: unused variable 'myTransMat' [-Wunused-variable]
double **myTransMat = this->A->getTransMat();
^
HMM.cpp: In member function 'void HMM::getDirScore(double*, int**, int*, int*, int*, int**, double***, double***, int, int, int*, int, double)':
HMM.cpp:432:13: warning: unused variable 'j' [-Wunused-variable]
int t,i,j,n,k;
^
HMM.cpp:432:17: warning: unused variable 'k' [-Wunused-variable]
int t,i,j,n,k;
^
HMM.cpp:451:9: warning: unused variable 'memory_used' [-Wunused-variable]
int memory_used = this->allocateMemEM(&emissionProb, &alpha, &beta, &gamma, &xsi, &c, &Pk, maxLen, nsample);
^
HMM.cpp:505:9: warning: unused variable 'memory_free' [-Wunused-variable]
int memory_free = this->deallocateMemEM(emissionProb, alpha, beta, gamma, xsi, c, Pk, maxLen, nsample);
^
HMM.cpp: In member function 'virtual void HMM::getGammaXsi(double**, double**, double*, double**, double**, double***, int*, int, int, double, int)':
HMM.cpp:576:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,t,k;
^
HMM.cpp: In member function 'virtual int HMM::deallocateMemEM(double**, double**, double**, double**, double***, double*, double*, int, int)':
HMM.cpp:696:11: warning: unused variable 'j' [-Wunused-variable]
int i,j,t;
^
HMM.cpp: In member function 'std::list<double> HMM::BaumWelch(double***, int*, int, int, int**, int*, int*, int*, int, int, int**, double***, SEXP, SEXP, int, double, double, int, int)':
HMM.cpp:1183:41: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(LENGTH(bidirOptimParams) > 0 & iter > 1)
^
HMM.cpp:1229:49: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(iter > 0 && LENGTH(bidirOptimParams) != 0 & now != before & DEBUG)
^
HMM.cpp:969:13: warning: unused variable 'j' [-Wunused-variable]
int t,i,j,n;
^
HMM.cpp:977:12: warning: unused variable 'old_prior' [-Wunused-variable]
double old_prior = -(double)INFINITY;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c InitialProbability.cpp -o InitialProbability.o
InitialProbability.cpp: In constructor 'InitialProbability::InitialProbability(double*, int)':
InitialProbability.cpp:17:75: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
printf("new->InitialProbability; (%d bytes)\n", sizeof(double)*K*2);
^
InitialProbability.cpp: In destructor 'virtual InitialProbability::˜InitialProbability()':
InitialProbability.cpp:30:78: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
printf("delete->InitialProbability; (%d bytes)\n", sizeof(double)*K*2);
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c JointlyIndependent.cpp -o JointlyIndependent.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c MemoryAllocation.cpp -o MemoryAllocation.o
MemoryAllocation.cpp: In function 'int allocateMemRescFac(double**, int, int)':
MemoryAllocation.cpp:92:9: warning: unused variable 'i' [-Wunused-variable]
int i,t;
^
MemoryAllocation.cpp: In function 'int allocateMemEmissionProb(double***, int, int)':
MemoryAllocation.cpp:184:11: warning: unused variable 'j' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp: In function 'int deallocateMemAlpha(double**, int, int)':
MemoryAllocation.cpp:215:9: warning: unused variable 'i' [-Wunused-variable]
int i,t;
^
MemoryAllocation.cpp: In function 'int deallocateMemBeta(double**, int, int)':
MemoryAllocation.cpp:233:9: warning: unused variable 'i' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp:233:11: warning: unused variable 'j' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp: In function 'int deallocateMemRescFac(double*, int, int)':
MemoryAllocation.cpp:252:9: warning: unused variable 'i' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp:252:11: warning: unused variable 'j' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp:252:13: warning: unused variable 't' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp: In function 'int deallocateMemGamma(double**, int, int)':
MemoryAllocation.cpp:265:9: warning: unused variable 'i' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp:265:11: warning: unused variable 'j' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp: In function 'int deallocateMemXsi(double***, int, int)':
MemoryAllocation.cpp:285:11: warning: unused variable 'j' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp: In function 'int deallocateMemEmissionProb(double**, int, int)':
MemoryAllocation.cpp:309:11: warning: unused variable 'j' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp:309:13: warning: unused variable 't' [-Wunused-variable]
int i,j,t;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c Multinomial.cpp -o Multinomial.o
Multinomial.cpp: In constructor 'Multinomial::Multinomial(ParamContainerEmissions*)':
Multinomial.cpp:26:13: warning: unused variable 'd2' [-Wunused-variable]
int d1, d2;
^
Multinomial.cpp: In destructor 'virtual Multinomial::˜Multinomial()':
Multinomial.cpp:38:9: warning: unused variable 'd1' [-Wunused-variable]
int d1;
^
Multinomial.cpp: In member function 'virtual double Multinomial::calcEmissionProbability(double*, int, int)':
Multinomial.cpp:58:12: warning: unused variable 'mult_coeff' [-Wunused-variable]
double mult_coeff = 0;
^
Multinomial.cpp: In member function 'virtual void Multinomial::updateAuxiliaries(double***, double**, double*, int*, int, int, int**)':
Multinomial.cpp:154:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d, obs_d_revcomp;
^
Multinomial.cpp: In member function 'virtual void Multinomial::updateAuxiliariesCoupledRevop(double***, double**, double*, int*, int, int, int, int*, int*, int**)':
Multinomial.cpp:212:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d,obs_d_revcomp;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c MultivariateGaussian.cpp -o MultivariateGaussian.o
MultivariateGaussian.cpp: In member function 'virtual void MultivariateGaussian::updateAuxiliaries(double***, double**, double*, int*, int, int, int**)':
MultivariateGaussian.cpp:136:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l;
^
MultivariateGaussian.cpp: In member function 'virtual void MultivariateGaussian::updateAuxiliariesCoupled(double***, double**, double*, int*, int, int, int, int**)':
MultivariateGaussian.cpp:169:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
MultivariateGaussian.cpp: In member function 'virtual void MultivariateGaussian::updateAuxiliariesCoupledRevop(double***, double**, double*, int*, int, int, int, int*, int*, int**)':
MultivariateGaussian.cpp:203:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
MultivariateGaussian.cpp: In member function 'virtual void MultivariateGaussian::updateCoupledRevop(double***, double*, int, int*, int*, double**, int**, SEXP, int, int)':
MultivariateGaussian.cpp:337:32: warning: unused variable 'l' [-Wunused-variable]
int t, l;
^
MultivariateGaussian.cpp:251:9: warning: unused variable 'skipcounter' [-Wunused-variable]
int skipcounter = 0;
^
MultivariateGaussian.cpp:265:12: warning: unused variable 'numer' [-Wunused-variable]
double numer, denom;
^
MultivariateGaussian.cpp:265:19: warning: unused variable 'denom' [-Wunused-variable]
double numer, denom;
^
MultivariateGaussian.cpp: In member function 'virtual void MultivariateGaussian::update(double***, double*, int**, SEXP, int, int)':
MultivariateGaussian.cpp:518:32: warning: unused variable 'l' [-Wunused-variable]
int t, l;
^
MultivariateGaussian.cpp:445:12: warning: unused variable 'numer' [-Wunused-variable]
double numer, denom;
^
MultivariateGaussian.cpp:445:19: warning: unused variable 'denom' [-Wunused-variable]
double numer, denom;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c NegativeBinomial.cpp -o NegativeBinomial.o
NegativeBinomial.cpp: In destructor 'virtual NegativeBinomial::˜NegativeBinomial()':
NegativeBinomial.cpp:36:9: warning: unused variable 'd1' [-Wunused-variable]
int d1;
^
NegativeBinomial.cpp: In member function 'virtual double NegativeBinomial::calcEmissionProbability(double*, int, int)':
NegativeBinomial.cpp:55:13: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
if(isna == -1 | isna == 1)
^
NegativeBinomial.cpp: In member function 'virtual void NegativeBinomial::updateCoupledRevop(double***, double*, int, int*, int*, double**, int**, SEXP, int, int)':
NegativeBinomial.cpp:438:13: warning: unused variable 'nsample' [-Wunused-variable]
int nsample = this->getParameter()->getN();
^
NegativeBinomial.cpp:439:13: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->getParameter()->getD();
^
NegativeBinomial.cpp:174:10: warning: unused variable 'myObs' [-Wunused-variable]
SEXP myObs, pars, myGammas, myd;
^
NegativeBinomial.cpp:176:9: warning: unused variable 'd' [-Wunused-variable]
int d;
^
NegativeBinomial.cpp:191:9: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->emissionParams->getD();
^
NegativeBinomial.cpp:433:9: warning: unused variable 'i' [-Wunused-variable]
int i,j;
^
NegativeBinomial.cpp: In member function 'virtual double NegativeBinomial::Prior(SEXP)':
NegativeBinomial.cpp:462:9: warning: unused variable 'i' [-Wunused-variable]
int i, j;
^
NegativeBinomial.cpp:462:12: warning: unused variable 'j' [-Wunused-variable]
int i, j;
^
NegativeBinomial.cpp: In member function 'virtual void NegativeBinomial::update(double***, double*, int**, SEXP, int, int)':
NegativeBinomial.cpp:601:13: warning: unused variable 'nsample' [-Wunused-variable]
int nsample = this->getParameter()->getN();
^
NegativeBinomial.cpp:602:13: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->getParameter()->getD();
^
NegativeBinomial.cpp:474:10: warning: unused variable 'myObs' [-Wunused-variable]
SEXP myObs, pars, myGammas, myd;
^
NegativeBinomial.cpp:483:9: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->emissionParams->getD();
^
NegativeBinomial.cpp:596:9: warning: unused variable 'i' [-Wunused-variable]
int i,j,d;
^
NegativeBinomial.cpp:596:13: warning: unused variable 'd' [-Wunused-variable]
int i,j,d;
^
NegativeBinomial.cpp: In member function 'virtual void NegativeBinomial::setParsToTwin(EmissionFunction*, int, double***)':
NegativeBinomial.cpp:639:13: warning: unused variable 'nsample' [-Wunused-variable]
int nsample = this->getParameter()->getN();
^
NegativeBinomial.cpp:640:13: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->getParameter()->getD();
^
NegativeBinomial.cpp:627:9: warning: unused variable 'i' [-Wunused-variable]
int i,j,d,n;
^
NegativeBinomial.cpp:627:13: warning: unused variable 'd' [-Wunused-variable]
int i,j,d,n;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
ParamContainerEmissions.cpp: In destructor 'virtual ParamContainerEmissions::˜ParamContainerEmissions()':
ParamContainerEmissions.cpp:212:13: warning: unused variable 'i' [-Wunused-variable]
int i;
^
ParamContainerEmissions.cpp:221:13: warning: unused variable 'i' [-Wunused-variable]
int i;
^
ParamContainerEmissions.cpp: In member function 'double ParamContainerEmissions::setMuNB(double)':
ParamContainerEmissions.cpp:650:1: warning: no return statement in function returning non-void [-Wreturn-type]
}
^
ParamContainerEmissions.cpp: In member function 'double ParamContainerEmissions::setSizeNB(double)':
ParamContainerEmissions.cpp:656:1: warning: no return statement in function returning non-void [-Wreturn-type]
}
^
ParamContainerEmissions.cpp: In member function 'double ParamContainerEmissions::setPiNB(double)':
ParamContainerEmissions.cpp:662:1: warning: no return statement in function returning non-void [-Wreturn-type]
}
^
ParamContainerEmissions.cpp: In member function 'double ParamContainerEmissions::setMuPoiLog(double)':
ParamContainerEmissions.cpp:692:1: warning: no return statement in function returning non-void [-Wreturn-type]
}
^
ParamContainerEmissions.cpp: In member function 'double ParamContainerEmissions::setSigmaPoiLog(double)':
ParamContainerEmissions.cpp:698:1: warning: no return statement in function returning non-void [-Wreturn-type]
}
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c Poisson.cpp -o Poisson.o
Poisson.cpp: In constructor 'Poisson::Poisson(ParamContainerEmissions*)':
Poisson.cpp:26:13: warning: unused variable 'd2' [-Wunused-variable]
int d1, d2;
^
Poisson.cpp: In destructor 'virtual Poisson::˜Poisson()':
Poisson.cpp:38:9: warning: unused variable 'd1' [-Wunused-variable]
int d1;
^
Poisson.cpp: In member function 'virtual void Poisson::updateAuxiliaries(double***, double**, double*, int*, int, int, int**)':
Poisson.cpp:101:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
Poisson.cpp: In member function 'virtual void Poisson::updateAuxiliariesCoupled(double***, double**, double*, int*, int, int, int, int**)':
Poisson.cpp:133:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
Poisson.cpp: In member function 'virtual void Poisson::updateAuxiliariesCoupledRevop(double***, double**, double*, int*, int, int, int, int*, int*, int**)':
Poisson.cpp:163:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
Poisson.cpp: In member function 'virtual void Poisson::updateCoupledRevop(double***, double*, int, int*, int*, double**, int**, SEXP, int, int)':
Poisson.cpp:211:9: warning: unused variable 'skipcounter' [-Wunused-variable]
int skipcounter = 0;
^
Poisson.cpp: In member function 'virtual void Poisson::update(double***, double*, int**, SEXP, int, int)':
Poisson.cpp:237:9: warning: unused variable 'skipcounter' [-Wunused-variable]
int skipcounter = 0;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c PoissonLogNormal.cpp -o PoissonLogNormal.o
PoissonLogNormal.cpp: In destructor 'virtual PoissonLogNormal::˜PoissonLogNormal()':
PoissonLogNormal.cpp:26:9: warning: unused variable 'd1' [-Wunused-variable]
int d1;
^
PoissonLogNormal.cpp: In member function 'virtual double PoissonLogNormal::calcEmissionProbability(double*, int, int)':
PoissonLogNormal.cpp:43:13: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
if(isna == -1 | isna == 1)
^
PoissonLogNormal.cpp: In member function 'virtual void PoissonLogNormal::updateCoupledRevop(double***, double*, int, int*, int*, double**, int**, SEXP, int, int)':
PoissonLogNormal.cpp:304:13: warning: unused variable 'nsample' [-Wunused-variable]
int nsample = this->getParameter()->getN();
^
PoissonLogNormal.cpp:305:13: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->getParameter()->getD();
^
PoissonLogNormal.cpp:135:10: warning: unused variable 'myObs' [-Wunused-variable]
SEXP myObs, pars, myGammas, myd;
^
PoissonLogNormal.cpp:135:17: warning: unused variable 'pars' [-Wunused-variable]
SEXP myObs, pars, myGammas, myd;
^
PoissonLogNormal.cpp:139:9: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->emissionParams->getD();
^
PoissonLogNormal.cpp:245:24: warning: unused variable 'PINB' [-Wunused-variable]
SEXP MUNB, SIZENB, PINB, CURRN, wname;
^
PoissonLogNormal.cpp:299:9: warning: unused variable 'i' [-Wunused-variable]
int i,j,d;
^
PoissonLogNormal.cpp:299:13: warning: unused variable 'd' [-Wunused-variable]
int i,j,d;
^
PoissonLogNormal.cpp: In member function 'virtual double PoissonLogNormal::Prior(SEXP)':
PoissonLogNormal.cpp:328:9: warning: unused variable 'i' [-Wunused-variable]
int i, j;
^
PoissonLogNormal.cpp:328:12: warning: unused variable 'j' [-Wunused-variable]
int i, j;
^
PoissonLogNormal.cpp: In member function 'virtual void PoissonLogNormal::update(double***, double*, int**, SEXP, int, int)':
PoissonLogNormal.cpp:438:13: warning: unused variable 'nsample' [-Wunused-variable]
int nsample = this->getParameter()->getN();
^
PoissonLogNormal.cpp:439:13: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->getParameter()->getD();
^
PoissonLogNormal.cpp:340:10: warning: unused variable 'myObs' [-Wunused-variable]
SEXP myObs, pars, myGammas, myd;
^
PoissonLogNormal.cpp:340:17: warning: unused variable 'pars' [-Wunused-variable]
SEXP myObs, pars, myGammas, myd;
^
PoissonLogNormal.cpp:345:9: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->emissionParams->getD();
^
PoissonLogNormal.cpp:379:24: warning: unused variable 'PINB' [-Wunused-variable]
SEXP MUNB, SIZENB, PINB, CURRN, wname;
^
PoissonLogNormal.cpp:433:9: warning: unused variable 'i' [-Wunused-variable]
int i,j,d;
^
PoissonLogNormal.cpp:433:13: warning: unused variable 'd' [-Wunused-variable]
int i,j,d;
^
PoissonLogNormal.cpp: In member function 'virtual void PoissonLogNormal::setParsToTwin(EmissionFunction*, int, double***)':
PoissonLogNormal.cpp:476:13: warning: unused variable 'nsample' [-Wunused-variable]
int nsample = this->getParameter()->getN();
^
PoissonLogNormal.cpp:477:13: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->getParameter()->getD();
^
PoissonLogNormal.cpp:464:9: warning: unused variable 'i' [-Wunused-variable]
int i,j,d,n;
^
PoissonLogNormal.cpp:464:13: warning: unused variable 'd' [-Wunused-variable]
int i,j,d,n;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c RAccessUtils.cpp -o RAccessUtils.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c RWrapper.cpp -o RWrapper.o
In file included from RWrapper.cpp:27:0:
EmissionFactory.h: In member function 'virtual EmissionFunction* EmissionFactory::createEmissionFunctionMixed(std::list<EmissionFunction*>, ParamContainerEmissions*)':
EmissionFactory.h:17:133: warning: no return statement in function returning non-void [-Wreturn-type]
virtual EmissionFunction* createEmissionFunctionMixed(list<EmissionFunction*> efb, ParamContainerEmissions *emissionParams){};
^
RWrapper.cpp: In function 'EmissionFunction** RGETMULTGAUSS(SEXP, SEXP, int, SEXP, int*, int, int)':
RWrapper.cpp:107:16: warning: deleting object of abstract class type 'EmissionFactory' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp: In function 'EmissionFunction** RGETBERNOULLI2(SEXP, int, SEXP, int*)':
RWrapper.cpp:129:16: warning: deleting object of abstract class type 'EmissionFactory' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp:114:13: warning: unused variable 'i' [-Wunused-variable]
int i,j,k;
^
RWrapper.cpp:114:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,k;
^
RWrapper.cpp: In function 'EmissionFunction** RGETPOISSON(SEXP, int, SEXP, int*)':
RWrapper.cpp:150:16: warning: deleting object of abstract class type 'EmissionFactory' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp:136:13: warning: unused variable 'i' [-Wunused-variable]
int i,j,k;
^
RWrapper.cpp:136:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,k;
^
RWrapper.cpp: In function 'EmissionFunction** RGETMULTINOMIAL(SEXP, SEXP, int, SEXP, int*, int*)':
RWrapper.cpp:189:16: warning: deleting object of abstract class type 'EmissionFactory' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp:157:13: warning: unused variable 'i' [-Wunused-variable]
int i,j,d,k;
^
RWrapper.cpp:157:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,d,k;
^
RWrapper.cpp: In function 'EmissionFunction** RGETNEGATIVEBINOMIAL(SEXP, SEXP, SEXP, SEXP, int, SEXP, int*, double***, int*, int, SEXP, int*)':
RWrapper.cpp:242:16: warning: deleting object of abstract class type 'EmissionFactory' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp:196:17: warning: unused variable 'd' [-Wunused-variable]
int i,j,d,k,n;
^
RWrapper.cpp: In function 'EmissionFunction** RGETPOISSONLOGNORMAL(SEXP, SEXP, SEXP, int, SEXP, int*, double***, int*, int, SEXP, int*)':
RWrapper.cpp:304:16: warning: deleting object of abstract class type 'EmissionFactory' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp:249:17: warning: unused variable 'd' [-Wunused-variable]
int i,j,d,k,n;
^
RWrapper.cpp: In function 'EmissionFunction** RGETBERNOULLI(SEXP, int, SEXP, int*, int)':
RWrapper.cpp:386:16: warning: deleting object of abstract class type 'EmissionFactory' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp:359:13: warning: unused variable 'i' [-Wunused-variable]
int i,j,k;
^
RWrapper.cpp:359:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,k;
^
RWrapper.cpp: In function 'SEXPREC* RPREPAREBERNOULLIPAR(EmissionFunction**, int)':
RWrapper.cpp:464:17: warning: unused variable 'j' [-Wunused-variable]
int k,i,j;
^
RWrapper.cpp: In function 'SEXPREC* RPREPAREBERNOULLIPAR2(EmissionFunction**, int, int)':
RWrapper.cpp:497:17: warning: unused variable 'j' [-Wunused-variable]
int k,d,j;
^
RWrapper.cpp: In function 'SEXPREC* RPREPAREPOISSONPAR(EmissionFunction**, int, int)':
RWrapper.cpp:530:17: warning: unused variable 'j' [-Wunused-variable]
int k,d,j;
^
RWrapper.cpp: In function 'SEXPREC* RPREPAREMULTINOMIALPAR(EmissionFunction**, int, int)':
RWrapper.cpp:563:17: warning: unused variable 'j' [-Wunused-variable]
int k,d,j;
^
RWrapper.cpp: In function 'SEXPREC* RPREPARENEGATIVEBINOMIALPAR(EmissionFunction**, int, int)':
RWrapper.cpp:609:17: warning: unused variable 'j' [-Wunused-variable]
int k,d,j;
^
RWrapper.cpp: In function 'SEXPREC* RPREPAREPOISSONLOGNORMALPAR(EmissionFunction**, int, int)':
RWrapper.cpp:666:17: warning: unused variable 'j' [-Wunused-variable]
int k,d,j;
^
RWrapper.cpp: In function 'EmissionFunction** createJointlyIndependent(std::list<EmissionFunction**>, int, SEXP, int*, int)':
RWrapper.cpp:811:17: warning: unused variable 'd' [-Wunused-variable]
int d = 0;
^
RWrapper.cpp:845:16: warning: deleting object of abstract class type 'EmissionFactory' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp:797:13: warning: unused variable 'i' [-Wunused-variable]
int i,j,k;
^
RWrapper.cpp:797:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,k;
^
RWrapper.cpp: In function 'void RFREEFLAGS(SEXP, SEXP, int**, int*, int)':
RWrapper.cpp:982:15: warning: unused variable 't' [-Wunused-variable]
int n,t,i;
^
RWrapper.cpp:982:17: warning: unused variable 'i' [-Wunused-variable]
int n,t,i;
^
RWrapper.cpp: In function 'EmissionFunction** getEmission(const char*, SEXP, SEXP, int*, int, int*, int, int, double***, int*, int*, int*)':
RWrapper.cpp:1083:21: warning: unused variable 'ordersize' [-Wunused-variable]
int ordersize;
^
RWrapper.cpp:1086:21: warning: unused variable 'currDim' [-Wunused-variable]
int currDim = length(currDims);
^
RWrapper.cpp:1049:21: warning: unused variable 'independent' [-Wunused-variable]
const char* independent = "Independent";
^
RWrapper.cpp:1052:21: warning: unused variable 'negativebinomial' [-Wunused-variable]
const char* negativebinomial = "NegativeBinomial";
^
RWrapper.cpp: In function 'SEXPREC* prepareEmission(const char*, SEXP, SEXP, EmissionFunction**, int)':
RWrapper.cpp:1128:21: warning: unused variable 'independent' [-Wunused-variable]
const char* independent = "Independent";
^
RWrapper.cpp:1132:21: warning: unused variable 'poissonlognormal' [-Wunused-variable]
const char* poissonlognormal = "PoissonLogNormal";
^
RWrapper.cpp: In function 'SEXPREC* RHMMVITERBI(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
RWrapper.cpp:1301:16: warning: deleting object of polymorphic class type 'HMM' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete myHMM;
^
RWrapper.cpp:1181:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,k,n,t;
^
RWrapper.cpp:1181:17: warning: unused variable 'k' [-Wunused-variable]
int i,j,k,n,t;
^
RWrapper.cpp: In function 'SEXPREC* RHMMFit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
RWrapper.cpp:1576:16: warning: deleting object of polymorphic class type 'HMM' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete myHMM;
^
RWrapper.cpp:1360:16: warning: unused variable 'regularize' [-Wunused-variable]
double regularize = REAL(sexpregularize)[0];
^
RWrapper.cpp:1362:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,k,n,t;
^
RWrapper.cpp:1362:17: warning: unused variable 'k' [-Wunused-variable]
int i,j,k,n,t;
^
RWrapper.cpp: In function 'SEXPREC* RGETPOSTERIOR(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
RWrapper.cpp:1828:16: warning: deleting object of polymorphic class type 'HMM' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete myHMM;
^
RWrapper.cpp:1664:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,k,n,t;
^
RWrapper.cpp:1664:17: warning: unused variable 'k' [-Wunused-variable]
int i,j,k,n,t;
^
RWrapper.cpp: In function 'SEXPREC* RGETLOGLIK(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
RWrapper.cpp:2040:16: warning: deleting object of polymorphic class type 'HMM' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete myHMM;
^
RWrapper.cpp:1886:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,k,n,t;
^
RWrapper.cpp:1886:17: warning: unused variable 'k' [-Wunused-variable]
int i,j,k,n,t;
^
RWrapper.cpp: In function 'SEXPREC* RPREPAREEMISSIONPAR(EmissionFunction**, int, const char*, int)':
RWrapper.cpp:742:5: warning: control reaches end of non-void function [-Wreturn-type]
}
^
RWrapper.cpp: In function 'HMM* createHMM(int, int, InitialProbability*, TransitionMatrix*, EmissionFunction**)':
RWrapper.cpp:951:5: warning: control reaches end of non-void function [-Wreturn-type]
}
^
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:1162:16: warning: 'sexpemissionParam' may be used uninitialized in this function [-Wmaybe-uninitialized]
return sexpemissionParam;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c TransitionMatrix.cpp -o TransitionMatrix.o
TransitionMatrix.cpp: In member function 'void TransitionMatrix::updateAuxiliaries(double**, double***, double*, int*, int, int*, SEXP, int**, int, double, int, int, int)':
TransitionMatrix.cpp:93:13: warning: unused variable 'k' [-Wunused-variable]
int i,j,k;
^
TransitionMatrix.cpp:94:19: warning: variable 'denom' set but not used [-Wunused-but-set-variable]
double numer, denom;
^
TransitionMatrix.cpp: In member function 'SEXPREC* TransitionMatrix::callRsolnp(SEXP)':
TransitionMatrix.cpp:673:14: warning: unused variable 'exwarn' [-Wunused-variable]
SEXP exwarn = PROTECT( eval( warn, R_GlobalEnv ) ) ;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=core2 -c matUtils.cpp -o matUtils.o
matUtils.cpp: In function 'void inverseR(double**, int)':
matUtils.cpp:62:10: warning: unused variable 'res' [-Wunused-variable]
SEXP res = PROTECT( eval( call, R_GlobalEnv ) ) ;
^
matUtils.cpp: In function 'void** matrixMult(double**, int, int, double**, int, int, double**)':
matUtils.cpp:99:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
C:/Rtools/mingw_64/bin/g++ -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˜1.6-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWSeBCR/Rinst1e7053bd135b/STAN/libs/x64
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for 'STAN' in namespaceExport(ns, exports):
undefined exports: initBdClust, fitBdClust
Error: loading failed
Execution halted
ERROR: loading failed
* removing 'C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWSeBCR/Rinst1e7053bd135b/STAN'
-----------------------------------
ERROR: package installation failed