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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MIMOSA
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MIMOSA' ...
** 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"C:/extsoft/include"  -I"D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c BetaMix.cpp -o BetaMix.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"C:/extsoft/include"  -I"D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c MCMC.cpp -o MCMC.o
MCMC.cpp: In function 'SEXPREC* fitMCMC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MCMC.cpp:73:9: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  if(file==NULL|fileP==NULL){
         ^
MCMC.cpp:88:18: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  if(alphas.size()!=stim.ncol()){
     ~~~~~~~~~~~~~^~~~~~~~~~~~~
MCMC.cpp:189:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for(int i=0;i<alphas.size();i++){
              ~^~~~~~~~~~~~~~
MCMC.cpp:192:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for(int i=0;i<alphau.size();i++){
              ~^~~~~~~~~~~~~~
MCMC.cpp:524:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
    for(int j=0;j<p.size();j++){
                ~^~~~~~~~~
MCMC.cpp:544:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
    for(int obs=0;obs<alphas.size();obs++){
                  ~~~^~~~~~~~~~~~~~
MCMC.cpp:547:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
    for(int obs=0;obs<alphau.size();obs++){
                  ~~~^~~~~~~~~~~~~~
MCMC.cpp: In function 'double lkbeta(const std::vector<double>&)':
MCMC.cpp:631:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for(int i=0;i<alpha.size();i++){
              ~^~~~~~~~~~~~~
MCMC.cpp: In function 'void simZ(double&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<bool>&, int, int)':
MCMC.cpp:681:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for(i=0;i < lnull.size(); i++){
          ~~^~~~~~~~~~~~~~
MCMC.cpp: In function 'double normconstIBeta(double, double, double, double)':
MCMC.cpp:815:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for(int i=0;i<upper.size();i++){
              ~^~~~~~~~~~~~~
MCMC.cpp: In function 'double nc(double, double, double, double, double)':
MCMC.cpp:888:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for(int i=0;i<(s.size()-1);i++){
              ~^~~~~~~~~~~~~
MCMC.cpp:893:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for(int i=0;i<s.size();i++){
              ~^~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -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"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c MIMOSA_init.c -o MIMOSA_init.o
"C:/rtools40/mingw64/bin/"gcc  -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"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c betaintegral.c -o betaintegral.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"C:/extsoft/include"  -I"D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c betaintegralRcpp.cpp -o betaintegralRcpp.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o MIMOSA.dll tmp.def BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -lm -lstdc++ -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -ID:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include -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-MIMOSA/00new/MIMOSA/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MIMOSA'
    finding HTML links ... done
    BetaMixResult-class                     html  
    ConstructMIMOSAExpressionSet            html  
    ICS                                     html  
    MDMix                                   html  
    MIMOSA-accessors                        html  
    MIMOSA-package                          html  
    MIMOSA                                  html  
    MIMOSAExpressionSet                     html  
    MIMOSAResult-class                      html  
    MIMOSAResult                            html  
    asinh_trans                             html  
    boxplotMIMOSAResultList                 html  
    combine.MIMOSA                          html  
    countsTable                             html  
    dot-fitMCMC                             html  
    fdr                                     html  
    getPosteriorResponseRate                html  
    pData-methods                           html  
    print                                   html  
    show                                    html  
    volcanoPlot                             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 (MIMOSA)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'isomiRs' is missing or broken
 done