##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data STAN
###
##############################################################################
##############################################################################
* checking for file ‘STAN/DESCRIPTION’ ... OK
* preparing ‘STAN’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘STAN’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c Bernoulli.cpp -o Bernoulli.o
Bernoulli.cpp:25:13: warning: unused variable 'd2' [-Wunused-variable]
int d1, d2;
^
Bernoulli.cpp:37:9: warning: unused variable 'd1' [-Wunused-variable]
int d1;
^
Bernoulli.cpp:60:12: warning: unused variable 'j' [-Wunused-variable]
int i, j, obs_i;
^
Bernoulli.cpp:99:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
Bernoulli.cpp:140:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
Bernoulli.cpp:170:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
Bernoulli.cpp:218:9: warning: unused variable 'skipcounter' [-Wunused-variable]
int skipcounter = 0;
^
Bernoulli.cpp:262:9: warning: unused variable 'skipcounter' [-Wunused-variable]
int skipcounter = 0;
^
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c EmissionFactory.cpp -o EmissionFactory.o
In file included from EmissionFactory.cpp:1:
./EmissionFactory.h:17:133: warning: control reaches end of non-void function [-Wreturn-type]
virtual EmissionFunction* createEmissionFunctionMixed(list<EmissionFunction*> efb, ParamContainerEmissions *emissionParams){};
^
In file included from EmissionFactory.cpp:2:
./MultivariateGaussianFactory.h:23:9: warning: control may reach end of non-void function [-Wreturn-type]
}
^
In file included from EmissionFactory.cpp:3:
./BernoulliFactory.h:27:9: warning: control may reach end of non-void function [-Wreturn-type]
}
^
In file included from EmissionFactory.cpp:4:
./PoissonFactory.h:24:9: warning: control may reach end of non-void function [-Wreturn-type]
}
^
In file included from EmissionFactory.cpp:5:
./MultinomialFactory.h:24:9: warning: control may reach end of non-void function [-Wreturn-type]
}
^
In file included from EmissionFactory.cpp:6:
./NegativeBinomialFactory.h:27:9: warning: control may reach end of non-void function [-Wreturn-type]
}
^
In file included from EmissionFactory.cpp:7:
./PoissonLogNormalFactory.h:27:9: warning: control may reach end of non-void function [-Wreturn-type]
}
^
In file included from EmissionFactory.cpp:8:
./JointlyIndependentFactory.h:28:17: warning: unused variable 'parallel' [-Wunused-variable]
int parallel=0;
^
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c EmissionFunction.cpp -o EmissionFunction.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c HMM.cpp -o HMM.o
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:112:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,t,k;
^
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: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:432:13: warning: unused variable 'j' [-Wunused-variable]
int t,i,j,n,k;
^
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: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:432:17: warning: unused variable 'k' [-Wunused-variable]
int t,i,j,n,k;
^
HMM.cpp:576:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,t,k;
^
HMM.cpp:696:11: warning: unused variable 'j' [-Wunused-variable]
int i,j,t;
^
HMM.cpp:977:12: warning: unused variable 'old_prior' [-Wunused-variable]
double old_prior = -(double)INFINITY;
^
HMM.cpp:969:13: warning: unused variable 'j' [-Wunused-variable]
int t,i,j,n;
^
16 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c InitialProbability.cpp -o InitialProbability.o
InitialProbability.cpp:17:57: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
printf("new->InitialProbability; (%d bytes)\n", sizeof(double)*K*2);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
%lu
InitialProbability.cpp:30:60: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
printf("delete->InitialProbability; (%d bytes)\n", sizeof(double)*K*2);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
%lu
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c JointlyIndependent.cpp -o JointlyIndependent.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c MemoryAllocation.cpp -o MemoryAllocation.o
MemoryAllocation.cpp:92:9: warning: unused variable 'i' [-Wunused-variable]
int i,t;
^
MemoryAllocation.cpp:184:11: warning: unused variable 'j' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp:215:9: warning: unused variable 'i' [-Wunused-variable]
int i,t;
^
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:252:13: warning: unused variable 't' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp:252:11: warning: unused variable 'j' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp:252:9: 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:265:9: warning: unused variable 'i' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp:285:11: warning: unused variable 'j' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp:309:13: warning: unused variable 't' [-Wunused-variable]
int i,j,t;
^
MemoryAllocation.cpp:309:11: warning: unused variable 'j' [-Wunused-variable]
int i,j,t;
^
13 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c Multinomial.cpp -o Multinomial.o
Multinomial.cpp:26:13: warning: unused variable 'd2' [-Wunused-variable]
int d1, d2;
^
Multinomial.cpp:38:9: warning: unused variable 'd1' [-Wunused-variable]
int d1;
^
Multinomial.cpp:58:12: warning: unused variable 'mult_coeff' [-Wunused-variable]
double mult_coeff = 0;
^
Multinomial.cpp:154:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d, obs_d_revcomp;
^
Multinomial.cpp:212:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d,obs_d_revcomp;
^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c MultivariateGaussian.cpp -o MultivariateGaussian.o
MultivariateGaussian.cpp:136:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l;
^
MultivariateGaussian.cpp:169:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
MultivariateGaussian.cpp:203:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
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:265:19: warning: unused variable 'denom' [-Wunused-variable]
double numer, denom;
^
MultivariateGaussian.cpp:265:12: warning: unused variable 'numer' [-Wunused-variable]
double numer, denom;
^
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;
^
10 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c NegativeBinomial.cpp -o NegativeBinomial.o
NegativeBinomial.cpp:36:9: warning: unused variable 'd1' [-Wunused-variable]
int d1;
^
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:176:9: warning: unused variable 'd' [-Wunused-variable]
int d;
^
NegativeBinomial.cpp:433:9: warning: unused variable 'i' [-Wunused-variable]
int i,j;
^
NegativeBinomial.cpp:174:10: warning: unused variable 'myObs' [-Wunused-variable]
SEXP myObs, pars, myGammas, myd;
^
NegativeBinomial.cpp:191:9: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->emissionParams->getD();
^
NegativeBinomial.cpp:462:12: warning: unused variable 'j' [-Wunused-variable]
int i, j;
^
NegativeBinomial.cpp:462:9: warning: unused variable 'i' [-Wunused-variable]
int i, j;
^
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:596:13: warning: unused variable 'd' [-Wunused-variable]
int i,j,d;
^
NegativeBinomial.cpp:474:10: warning: unused variable 'myObs' [-Wunused-variable]
SEXP myObs, pars, myGammas, myd;
^
NegativeBinomial.cpp:596:9: warning: unused variable 'i' [-Wunused-variable]
int i,j,d;
^
NegativeBinomial.cpp:483:9: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->emissionParams->getD();
^
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;
^
19 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
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:650:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
ParamContainerEmissions.cpp:656:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
ParamContainerEmissions.cpp:662:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
ParamContainerEmissions.cpp:692:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
ParamContainerEmissions.cpp:698:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
7 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c Poisson.cpp -o Poisson.o
Poisson.cpp:26:13: warning: unused variable 'd2' [-Wunused-variable]
int d1, d2;
^
Poisson.cpp:38:9: warning: unused variable 'd1' [-Wunused-variable]
int d1;
^
Poisson.cpp:101:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
Poisson.cpp:133:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
Poisson.cpp:163:15: warning: unused variable 'l' [-Wunused-variable]
int t, d, l, obs_d;
^
Poisson.cpp:211:9: warning: unused variable 'skipcounter' [-Wunused-variable]
int skipcounter = 0;
^
Poisson.cpp:237:9: warning: unused variable 'skipcounter' [-Wunused-variable]
int skipcounter = 0;
^
7 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c PoissonLogNormal.cpp -o PoissonLogNormal.o
PoissonLogNormal.cpp:26:9: warning: unused variable 'd1' [-Wunused-variable]
int d1;
^
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:135:17: warning: unused variable 'pars' [-Wunused-variable]
SEXP myObs, pars, myGammas, myd;
^
PoissonLogNormal.cpp:135:10: warning: unused variable 'myObs' [-Wunused-variable]
SEXP myObs, pars, myGammas, myd;
^
PoissonLogNormal.cpp:245:24: warning: unused variable 'PINB' [-Wunused-variable]
SEXP MUNB, SIZENB, PINB, CURRN, wname;
^
PoissonLogNormal.cpp:139:9: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->emissionParams->getD();
^
PoissonLogNormal.cpp:299:13: warning: unused variable 'd' [-Wunused-variable]
int i,j,d;
^
PoissonLogNormal.cpp:299:9: warning: unused variable 'i' [-Wunused-variable]
int i,j,d;
^
PoissonLogNormal.cpp:328:12: warning: unused variable 'j' [-Wunused-variable]
int i, j;
^
PoissonLogNormal.cpp:328:9: warning: unused variable 'i' [-Wunused-variable]
int i, j;
^
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:345:9: warning: unused variable 'myD' [-Wunused-variable]
int myD = this->emissionParams->getD();
^
PoissonLogNormal.cpp:433:13: warning: unused variable 'd' [-Wunused-variable]
int i,j,d;
^
PoissonLogNormal.cpp:433:9: warning: unused variable 'i' [-Wunused-variable]
int i,j,d;
^
PoissonLogNormal.cpp:340:17: warning: unused variable 'pars' [-Wunused-variable]
SEXP myObs, pars, myGammas, myd;
^
PoissonLogNormal.cpp:340:10: warning: unused variable 'myObs' [-Wunused-variable]
SEXP myObs, pars, myGammas, myd;
^
PoissonLogNormal.cpp:379:24: warning: unused variable 'PINB' [-Wunused-variable]
SEXP MUNB, SIZENB, PINB, CURRN, wname;
^
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:464:13: warning: unused variable 'd' [-Wunused-variable]
int i,j,d,n;
^
PoissonLogNormal.cpp:464:9: warning: unused variable 'i' [-Wunused-variable]
int i,j,d,n;
^
23 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c RAccessUtils.cpp -o RAccessUtils.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c RWrapper.cpp -o RWrapper.o
In file included from RWrapper.cpp:27:
./EmissionFactory.h:17:133: warning: control reaches end of non-void function [-Wreturn-type]
virtual EmissionFunction* createEmissionFunctionMixed(list<EmissionFunction*> efb, ParamContainerEmissions *emissionParams){};
^
RWrapper.cpp:107:9: warning: delete called on 'EmissionFactory' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp:129:9: warning: delete called on 'EmissionFactory' that is abstract but has non-virtual destructor [-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:150:9: warning: delete called on 'EmissionFactory' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp:136:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,k;
^
RWrapper.cpp:136:13: warning: unused variable 'i' [-Wunused-variable]
int i,j,k;
^
RWrapper.cpp:189:9: warning: delete called on 'EmissionFactory' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp:157:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,d,k;
^
RWrapper.cpp:157:13: warning: unused variable 'i' [-Wunused-variable]
int i,j,d,k;
^
RWrapper.cpp:242:9: warning: delete called on 'EmissionFactory' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp:196:17: warning: unused variable 'd' [-Wunused-variable]
int i,j,d,k,n;
^
RWrapper.cpp:304:9: warning: delete called on 'EmissionFactory' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp:249:17: warning: unused variable 'd' [-Wunused-variable]
int i,j,d,k,n;
^
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;
^
= NULL
RWrapper.cpp:386:9: warning: delete called on 'EmissionFactory' that is abstract but has non-virtual destructor [-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:464:17: warning: unused variable 'j' [-Wunused-variable]
int k,i,j;
^
RWrapper.cpp:497:17: warning: unused variable 'j' [-Wunused-variable]
int k,d,j;
^
RWrapper.cpp:530:17: warning: unused variable 'j' [-Wunused-variable]
int k,d,j;
^
RWrapper.cpp:563:17: warning: unused variable 'j' [-Wunused-variable]
int k,d,j;
^
RWrapper.cpp:609:17: warning: unused variable 'j' [-Wunused-variable]
int k,d,j;
^
RWrapper.cpp:666:17: warning: unused variable 'j' [-Wunused-variable]
int k,d,j;
^
RWrapper.cpp:742:5: warning: control may reach end of non-void function [-Wreturn-type]
}
^
RWrapper.cpp:811:17: warning: unused variable 'd' [-Wunused-variable]
int d = 0;
^
RWrapper.cpp:845:9: warning: delete called on 'EmissionFactory' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
delete factory;
^
RWrapper.cpp:797:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,k;
^
RWrapper.cpp:797:13: warning: unused variable 'i' [-Wunused-variable]
int i,j,k;
^
RWrapper.cpp:951:5: warning: control may reach end of non-void function [-Wreturn-type]
}
^
RWrapper.cpp:982:17: warning: unused variable 'i' [-Wunused-variable]
int n,t,i;
^
RWrapper.cpp:982:15: warning: unused variable 't' [-Wunused-variable]
int n,t,i;
^
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:1052:21: warning: unused variable 'negativebinomial' [-Wunused-variable]
const char* negativebinomial = "NegativeBinomial";
^
RWrapper.cpp:1049:21: warning: unused variable 'independent' [-Wunused-variable]
const char* independent = "Independent";
^
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:1145:21: warning: variable 'sexpemissionParam' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if(strcmp(type, multinomial) == 0)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:1162:16: note: uninitialized use occurs here
return sexpemissionParam;
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:1145:18: note: remove the 'if' if its condition is always true
else if(strcmp(type, multinomial) == 0)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:1126:31: note: initialize the variable 'sexpemissionParam' to silence this warning
SEXP sexpemissionParam;
^
= NULL
RWrapper.cpp:1301:9: warning: delete called on non-final 'HMM' that has virtual functions but non-virtual destructor [-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:1576:9: warning: delete called on non-final 'HMM' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
delete myHMM;
^
RWrapper.cpp:1360:16: warning: unused variable 'regularize' [-Wunused-variable]
double regularize = REAL(sexpregularize)[0];
^
RWrapper.cpp:1362:17: warning: unused variable 'k' [-Wunused-variable]
int i,j,k,n,t;
^
RWrapper.cpp:1362:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,k,n,t;
^
RWrapper.cpp:1828:9: warning: delete called on non-final 'HMM' that has virtual functions but non-virtual destructor [-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:2040:9: warning: delete called on non-final 'HMM' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
delete myHMM;
^
RWrapper.cpp:1886:17: warning: unused variable 'k' [-Wunused-variable]
int i,j,k,n,t;
^
RWrapper.cpp:1886:15: warning: unused variable 'j' [-Wunused-variable]
int i,j,k,n,t;
^
53 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c TransitionMatrix.cpp -o TransitionMatrix.o
TransitionMatrix.cpp:93:13: warning: unused variable 'k' [-Wunused-variable]
int i,j,k;
^
TransitionMatrix.cpp:673:14: warning: unused variable 'exwarn' [-Wunused-variable]
SEXP exwarn = PROTECT( eval( warn, R_GlobalEnv ) ) ;
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fPIC -Wall -g -O2 -c matUtils.cpp -o matUtils.o
matUtils.cpp:41:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete IPIV;
^
[]
matUtils.cpp:16:17: note: allocated with 'new[]' here
int *IPIV = new int[N+1];
^
matUtils.cpp:42:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete WORK;
^
[]
matUtils.cpp:18:20: note: allocated with 'new[]' here
double *WORK = new double[LWORK];
^
matUtils.cpp:62:10: warning: unused variable 'res' [-Wunused-variable]
SEXP res = PROTECT( eval( call, R_GlobalEnv ) ) ;
^
matUtils.cpp:99:1: warning: control may reach end of non-void function [-Wreturn-type]
}
^
matUtils.cpp:130:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete myAP;
^
[]
matUtils.cpp:106:21: note: allocated with 'new[]' here
double *myAP = new double[myNCol*(myNCol + 1)/2],
^
matUtils.cpp:131:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete myW;
^
[]
matUtils.cpp:107:16: note: allocated with 'new[]' here
*myW = new double[myNCol],
^
matUtils.cpp:132:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete myZ;
^
[]
matUtils.cpp:108:16: note: allocated with 'new[]' here
*myZ = new double[myNCol*myNCol],
^
matUtils.cpp:133:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete myWork;
^
[]
matUtils.cpp:109:19: note: allocated with 'new[]' here
*myWork = new double[myNCol * 3] ;
^
8 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /private/tmp/Rtmp8tHq94/Rinstb297ebff7ef/STAN/libs
** 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 '/private/tmp/Rtmp8tHq94/Rinstb297ebff7ef/STAN'
-----------------------------------
ERROR: package installation failed