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CHECK report for STAN on malbec1

This page was generated on 2018-04-12 13:12:30 -0400 (Thu, 12 Apr 2018).

Package 1354/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.6.0
Rafael Campos-Martin
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/STAN
Branch: RELEASE_3_6
Last Commit: bce95ec
Last Changed Date: 2017-10-30 12:40:20 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: STAN
Version: 2.6.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings STAN_2.6.0.tar.gz
StartedAt: 2018-04-12 03:10:39 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:15:05 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 265.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: STAN.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings STAN_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/STAN.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STAN/DESCRIPTION’ ... OK
* this is package ‘STAN’ version ‘2.6.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘STAN’ can be installed ... WARNING
Found the following significant warnings:
  EmissionFactory.h:17:133: warning: no return statement in function returning non-void [-Wreturn-type]
  MultivariateGaussianFactory.h:23:9: warning: control reaches end of non-void function [-Wreturn-type]
  BernoulliFactory.h:27:9: warning: control reaches end of non-void function [-Wreturn-type]
  PoissonFactory.h:24:9: warning: control reaches end of non-void function [-Wreturn-type]
  MultinomialFactory.h:24:9: warning: control reaches end of non-void function [-Wreturn-type]
  NegativeBinomialFactory.h:27:9: warning: control reaches end of non-void function [-Wreturn-type]
  PoissonLogNormalFactory.h:27:9: warning: control reaches end of non-void function [-Wreturn-type]
  ParamContainerEmissions.cpp:651:1: warning: no return statement in function returning non-void [-Wreturn-type]
  ParamContainerEmissions.cpp:657:1: warning: no return statement in function returning non-void [-Wreturn-type]
  ParamContainerEmissions.cpp:663:1: warning: no return statement in function returning non-void [-Wreturn-type]
  ParamContainerEmissions.cpp:693:1: warning: no return statement in function returning non-void [-Wreturn-type]
  ParamContainerEmissions.cpp:699:1: warning: no return statement in function returning non-void [-Wreturn-type]
  RWrapper.cpp:742:5: warning: control reaches end of non-void function [-Wreturn-type]
  RWrapper.cpp:951:5: warning: control reaches end of non-void function [-Wreturn-type]
  matUtils.cpp:99:1: warning: control reaches end of non-void function [-Wreturn-type]
See ‘/home/biocbuild/bbs-3.6-bioc/meat/STAN.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
initBdClust: warning in initBdHMM(obs, dStates = dStates, uStates =
  uStates, method = method, directedObs = directedObs, sizeFactor =
  sizeFactors, sharedCov = sharedCov, dirFlags = dirFlags): partial
  argument match of 'sizeFactor' to 'sizeFactors'
binarizeData : <anonymous>: no visible global function definition for
  'ppois'
clusterMat : <anonymous>: no visible global function definition for
  'ppois'
clusterMat: no visible global function definition for 'kmeans'
myQNBinom: no visible global function definition for 'dnbinom'
optimizeNB : <anonymous>: no visible global function definition for
  'optim'
optimizeNBInit: no visible global function definition for 'optim'
optimizePoiLog : <anonymous>: no visible global function definition for
  'optim'
optimizePoiLogInit: no visible global function definition for 'optim'
Undefined global functions or variables:
  dnbinom kmeans optim ppois
Consider adding
  importFrom("stats", "dnbinom", "kmeans", "optim", "ppois")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
viterbi2GRanges 18.872  0.136   2.652
getAvgSignal    18.744  0.168   2.458
fitBdClust      10.908  0.080   1.464
DirScore         9.088  0.084   2.421
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/STAN.Rcheck/00check.log’
for details.

Installation output

STAN.Rcheck/00install.out

* installing *source* package ‘STAN’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -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;
         ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c EmissionFactory.cpp -o EmissionFactory.o
In file included from EmissionFactory.cpp:1:0:
EmissionFactory.h: In member function ‘virtual EmissionFunction* EmissionFactory::createEmissionFunctionMixed(std::__cxx11::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::__cxx11::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]
         }
         ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c EmissionFunction.cpp -o EmissionFunction.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -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::__cxx11::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;
            ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -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 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 unsigned int’ [-Wformat=]
         printf("delete->InitialProbability; (%d bytes)\n", sizeof(double)*K*2);
                                                                              ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c JointlyIndependent.cpp -o JointlyIndependent.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -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;
             ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -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;
               ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -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;
                   ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -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:439:13: warning: unused variable ‘nsample’ [-Wunused-variable]
         int nsample =  this->getParameter()->getN();
             ^
NegativeBinomial.cpp:440:13: warning: unused variable ‘myD’ [-Wunused-variable]
         int myD =  this->getParameter()->getD();
             ^
NegativeBinomial.cpp:175:10: warning: unused variable ‘myObs’ [-Wunused-variable]
     SEXP myObs, pars, myGammas, myd;
          ^
NegativeBinomial.cpp:177:9: warning: unused variable ‘d’ [-Wunused-variable]
     int d;
         ^
NegativeBinomial.cpp:192:9: warning: unused variable ‘myD’ [-Wunused-variable]
     int myD = this->emissionParams->getD();
         ^
NegativeBinomial.cpp:434:9: warning: unused variable ‘i’ [-Wunused-variable]
     int i,j;
         ^
NegativeBinomial.cpp: In member function ‘virtual double NegativeBinomial::Prior(SEXP)’:
NegativeBinomial.cpp:463:9: warning: unused variable ‘i’ [-Wunused-variable]
     int i, j;
         ^
NegativeBinomial.cpp:463:12: 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:602:13: warning: unused variable ‘nsample’ [-Wunused-variable]
         int nsample =  this->getParameter()->getN();
             ^
NegativeBinomial.cpp:603:13: warning: unused variable ‘myD’ [-Wunused-variable]
         int myD =  this->getParameter()->getD();
             ^
NegativeBinomial.cpp:475:10: warning: unused variable ‘myObs’ [-Wunused-variable]
     SEXP myObs, pars, myGammas, myd;
          ^
NegativeBinomial.cpp:484:9: warning: unused variable ‘myD’ [-Wunused-variable]
     int myD = this->emissionParams->getD();
         ^
NegativeBinomial.cpp:597:9: warning: unused variable ‘i’ [-Wunused-variable]
     int i,j,d;
         ^
NegativeBinomial.cpp:597:13: warning: unused variable ‘d’ [-Wunused-variable]
     int i,j,d;
             ^
NegativeBinomial.cpp: In member function ‘virtual void NegativeBinomial::setParsToTwin(EmissionFunction*, int, double***)’:
NegativeBinomial.cpp:640:13: warning: unused variable ‘nsample’ [-Wunused-variable]
         int nsample =  this->getParameter()->getN();
             ^
NegativeBinomial.cpp:641:13: warning: unused variable ‘myD’ [-Wunused-variable]
         int myD =  this->getParameter()->getD();
             ^
NegativeBinomial.cpp:628:9: warning: unused variable ‘i’ [-Wunused-variable]
     int i,j,d,n;
         ^
NegativeBinomial.cpp:628:13: warning: unused variable ‘d’ [-Wunused-variable]
     int i,j,d,n;
             ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -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:651:1: warning: no return statement in function returning non-void [-Wreturn-type]
 }
 ^
ParamContainerEmissions.cpp: In member function ‘double ParamContainerEmissions::setSizeNB(double)’:
ParamContainerEmissions.cpp:657:1: warning: no return statement in function returning non-void [-Wreturn-type]
 }
 ^
ParamContainerEmissions.cpp: In member function ‘double ParamContainerEmissions::setPiNB(double)’:
ParamContainerEmissions.cpp:663:1: warning: no return statement in function returning non-void [-Wreturn-type]
 }
 ^
ParamContainerEmissions.cpp: In member function ‘double ParamContainerEmissions::setMuPoiLog(double)’:
ParamContainerEmissions.cpp:693:1: warning: no return statement in function returning non-void [-Wreturn-type]
 }
 ^
ParamContainerEmissions.cpp: In member function ‘double ParamContainerEmissions::setSigmaPoiLog(double)’:
ParamContainerEmissions.cpp:699:1: warning: no return statement in function returning non-void [-Wreturn-type]
 }
 ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -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;
         ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -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;
             ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c RAccessUtils.cpp -o RAccessUtils.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c RWrapper.cpp -o RWrapper.o
In file included from RWrapper.cpp:27:0:
EmissionFactory.h: In member function ‘virtual EmissionFunction* EmissionFactory::createEmissionFunctionMixed(std::__cxx11::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::__cxx11::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;
                ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -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 ) ) ;
              ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -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]
 }
 ^
g++ -shared -L/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/STAN.Rcheck/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
* DONE (STAN)

Tests output

Example timings

STAN.Rcheck/STAN-Ex.timings

nameusersystemelapsed
DimNames0.0080.0000.005
DirScore9.0880.0842.421
Emission0.0040.0000.003
EmissionParams0.0040.0000.004
HMM-class0.0040.0000.003
HMM0.0160.0000.019
HMMEmission-class0.0000.0000.002
HMMEmission0.0000.0000.003
InitProb0.0040.0000.002
LogLik3.0800.0240.411
StateNames0.0040.0000.004
Transitions0.0040.0000.004
bdHMM-class0.0640.0120.080
bdHMM0.0160.0000.016
binarizeData0.0440.0080.053
call_dpoilog0.0000.0000.001
fitBdClust10.908 0.080 1.464
fitHMM2.8480.0400.407
getAvgSignal18.744 0.168 2.458
getLogLik3.4760.0360.401
getPosterior3.3080.0480.356
getSizeFactors0.0600.0040.057
getViterbi3.5960.0560.539
initBdHMM0.0160.0000.017
initHMM0.0160.0000.014
runningMean0.0600.0080.068
viterbi2GRanges18.872 0.136 2.652