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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GeoDiff
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'GeoDiff' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/roptim/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c NBthDEOptPara.cpp -o NBthDEOptPara.o
NBthDEOptPara.cpp: In member function 'virtual double NBthDE_paranll::operator()(const vec&)':
NBthDEOptPara.cpp:34:9: warning: unused variable 'm' [-Wunused-variable]
     int m = y.n_elem;
         ^
NBthDEOptPara.cpp: In member function 'virtual void NBthDE_paranll::Gradient(const vec&, arma::vec&)':
NBthDEOptPara.cpp:85:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int k = 0; k < y.n_elem; k++){
                    ~~^~~~~~~~~~
NBthDEOptPara.cpp:58:9: warning: unused variable 'm' [-Wunused-variable]
     int m = y.n_elem;
         ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/roptim/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c NBthmDEGrad.cpp -o NBthmDEGrad.o
NBthmDEGrad.cpp: In function 'arma::vec NBthmDE_grad(arma::vec&, arma::mat&, arma::mat&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::mat&, double, double)':
NBthmDEGrad.cpp:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i = 0; i < y.n_elem; i++){
                  ~~^~~~~~~~~~
NBthmDEGrad.cpp: In function 'arma::mat NBthmDE_gradM(arma::vec&, arma::mat&, arma::mat&, arma::vec&, arma::mat&, arma::vec&, arma::vec&, arma::mat&, double, double)':
NBthmDEGrad.cpp:90:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int k = 0; k < y.n_elem; k++){
                      ~~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/roptim/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c NBthmDEMH.cpp -o NBthmDEMH.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/roptim/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c NBthmDEOptPara.cpp -o NBthmDEOptPara.o
NBthmDEOptPara.cpp: In member function 'virtual void NBthmDE_fparanll::Gradient(const vec&, arma::vec&)':
NBthmDEOptPara.cpp:107:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int k = 0; k < y.n_elem; k++){
                      ~~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/roptim/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c NBthmDEOptU.cpp -o NBthmDEOptU.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/roptim/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c PoisthNormOptPara.cpp -o PoisthNormOptPara.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/roptim/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/roptim/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c dnbinom_mu_vec.cpp -o dnbinom_mu_vec.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o GeoDiff.dll tmp.def NBthDEOptPara.o NBthmDEGrad.o NBthmDEMH.o NBthmDEOptPara.o NBthmDEOptU.o PoisthNormOptPara.o RcppExports.o dnbinom_mu_vec.o -fopenmp -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GeoDiff/00new/GeoDiff/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GeoDiff'
    finding HTML links ... done
    BGScoreTest-methods                     html  
    BGScoreTest_sp-methods                  html  
    DENBth-methods                          html  
    NBthDEmod2                              html  
    NBthmDEmod2                             html  
    NBthmDEmod2slope                        html  
    QuanRange-methods                       html  
    aggreprobe-methods                      html  
    coefNBth-methods                        html  
    contrastNBth-methods                    html  
    demoData                                html  
    diagPoisBG-methods                      html  
    fitNBth-methods                         html  
    fitNBthDE-methods                       html  
    fitNBthmDE-methods                      html  
    fitPoisBG-methods                       html  
    fitPoisBG_sp-methods                    html  
    fitPoisthNorm-methods                   html  
    fitPoisthNorm_sp-methods                html  
    kidney                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GeoDiff)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'kebabs' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'Rmagpie' is missing or broken
 done