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CHECK report for STAN on tokay1

This page was generated on 2018-04-12 13:24:41 -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: rm -rf STAN.buildbin-libdir STAN.Rcheck && mkdir STAN.buildbin-libdir STAN.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=STAN.buildbin-libdir STAN_2.6.0.tar.gz >STAN.Rcheck\00install.out 2>&1 && cp STAN.Rcheck\00install.out STAN-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=STAN.buildbin-libdir --install="check:STAN-install.out" --force-multiarch --no-vignettes --timings STAN_2.6.0.tar.gz
StartedAt: 2018-04-12 03:25:37 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:32:28 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 411.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: STAN.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   rm -rf STAN.buildbin-libdir STAN.Rcheck && mkdir STAN.buildbin-libdir STAN.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=STAN.buildbin-libdir STAN_2.6.0.tar.gz >STAN.Rcheck\00install.out 2>&1 && cp STAN.Rcheck\00install.out STAN-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=STAN.buildbin-libdir --install="check:STAN-install.out" --force-multiarch --no-vignettes --timings STAN_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/STAN.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 'C:/Users/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/STAN.buildbin-libdir/STAN/libs/i386/STAN.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/STAN.Rcheck/00check.log'
for details.

Installation output

STAN.Rcheck/00install.out


install for i386

* installing *source* package 'STAN' ...
** libs
C:/Rtools/mingw_32/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=generic -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_32/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=generic -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_32/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=generic -c EmissionFunction.cpp -o EmissionFunction.o
C:/Rtools/mingw_32/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=generic -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_32/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=generic -c InitialProbability.cpp -o InitialProbability.o
C:/Rtools/mingw_32/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=generic -c JointlyIndependent.cpp -o JointlyIndependent.o
C:/Rtools/mingw_32/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=generic -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_32/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=generic -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_32/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=generic -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_32/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=generic -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;
             ^
C:/Rtools/mingw_32/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=generic -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]
 }
 ^
C:/Rtools/mingw_32/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=generic -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_32/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=generic -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_32/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=generic -c RAccessUtils.cpp -o RAccessUtils.o
C:/Rtools/mingw_32/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=generic -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_32/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=generic -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_32/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=generic -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_32/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/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/STAN.buildbin-libdir/STAN/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'STAN'
    finding HTML links ... done
    DimNames                                html  
    DirScore                                html  
    Emission                                html  
    EmissionParams                          html  
    HMM-class                               html  
    HMM                                     html  
    HMMEmission-class                       html  
    HMMEmission                             html  
    InitProb                                html  
    LogLik                                  html  
    STAN-package                            html  
    StateNames                              html  
    Transitions                             html  
    bdHMM-class                             html  
    bdHMM                                   html  
    binarizeData                            html  
    c2optimize                              html  
    call_dpoilog                            html  
    data2Gviz                               html  
    example                                 html  
    fitBdClust                              html  
    fitHMM                                  html  
    flags                                   html  
    getAvgSignal                            html  
    getLogLik                               html  
    getPosterior                            html  
    getSizeFactors                          html  
    getViterbi                              html  
    initBdClust                             html  
    initBdHMM                               html  
    initHMM                                 html  
    observations                            html  
    pilot.hg19                              html  
    runningMean                             html  
    sub-HMM-ANY-ANY-ANY-method              html  
    sub-bdHMM-ANY-ANY-ANY-method            html  
    trainRegions                            html  
    ucscGenes                               html  
    viterbi2GRanges                         html  
    viterbi2Gviz                            html  
    yeastTF_SGDGenes                        html  
    yeastTF_databychrom_ex                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* 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=generic -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=generic -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=generic -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=generic -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=generic -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=generic -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=generic -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=generic -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=generic -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=generic -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;
             ^
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=generic -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]
 }
 ^
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=generic -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=generic -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=generic -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=generic -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=generic -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=generic -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/meat/STAN.buildbin-libdir/STAN/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'STAN' as STAN_2.6.0.zip
* DONE (STAN)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

STAN.Rcheck/examples_i386/STAN-Ex.timings

nameusersystemelapsed
DimNames0.000.010.01
DirScore1.450.131.58
Emission000
EmissionParams000
HMM-class0.010.000.02
HMM0.020.000.01
HMMEmission-class0.010.000.02
HMMEmission000
InitProb000
LogLik0.080.010.14
StateNames000
Transitions000
bdHMM-class0.060.000.06
bdHMM000
binarizeData0.080.010.09
call_dpoilog000
fitBdClust0.440.020.45
fitHMM0.110.030.18
getAvgSignal1.090.161.01
getLogLik0.030.000.06
getPosterior0.070.010.10
getSizeFactors0.060.000.07
getViterbi0.130.030.17
initBdHMM0.010.000.01
initHMM000
runningMean0.070.020.08
viterbi2GRanges1.180.011.27

STAN.Rcheck/examples_x64/STAN-Ex.timings

nameusersystemelapsed
DimNames000
DirScore1.330.041.44
Emission000
EmissionParams0.010.000.02
HMM-class000
HMM0.020.000.01
HMMEmission-class000
HMMEmission000
InitProb0.020.000.02
LogLik0.060.000.11
StateNames000
Transitions000
bdHMM-class0.040.000.04
bdHMM0.020.000.02
binarizeData0.020.010.03
call_dpoilog000
fitBdClust0.330.080.34
fitHMM0.170.000.14
getAvgSignal0.800.080.80
getLogLik0.010.000.06
getPosterior0.050.030.08
getSizeFactors0.050.000.04
getViterbi0.120.000.16
initBdHMM0.000.010.02
initHMM0.000.020.01
runningMean0.070.000.06
viterbi2GRanges1.010.081.05