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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/openCyto_2.6.0.tar.gz && rm -rf openCyto.buildbin-libdir && mkdir openCyto.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openCyto.buildbin-libdir openCyto_2.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL openCyto_2.6.0.zip && rm openCyto_2.6.0.tar.gz openCyto_2.6.0.zip
###
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install for i386

* installing *source* package 'openCyto' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cpPmden.cpp -o cpPmden.o
cpPmden.cpp: In function 'stringInfo cpPmden(const std::vector<double>&)':
cpPmden.cpp:88:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
   for (auto i = 0; i < (nsamp-1); i++) {
                    ~~^~~~~~~~~~~
cpPmden.cpp:100:17: warning: variable 'newaccx' set but not used [-Wunused-but-set-variable]
     double rhs, newaccx;
                 ^~~~~~~
cpPmden.cpp:157:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     for (auto i = 0; i < nsamp; i++) {
                      ~~^~~~~~~
cpPmden.cpp:164:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     for (auto i=0; i < (nsamp-2); i++) {
                    ~~^~~~~~~~~~~
cpPmden.cpp:193:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     for (auto i = 0; i < nsamp; i++) {
                      ~~^~~~~~~
cpPmden.cpp:219:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
       for (auto i = 0; i < nsamp; i++) {
                        ~~^~~~~~~
cpPmden.cpp:251:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
       for (auto i = 0; i < nsamp; i++) {
                        ~~^~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cppApprox.cpp -o cppApprox.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cppdip.cpp -o cppdip.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dynamic_prog.cpp -o dynamic_prog.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fill_SMAWK.cpp -o fill_SMAWK.o
fill_SMAWK.cpp: In function 'void reduce_in_place(int, int, int, int, const std::vector<unsigned int>&, std::vector<unsigned int>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)':
fill_SMAWK.cpp:80:8: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<unsigned int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   if(N >= js.size()) {
      ~~^~~~~~~~~~~~
fill_SMAWK.cpp:90:11: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   while(m > N) { // js_reduced has more than N positions / columns
         ~~^~~
fill_SMAWK.cpp:121:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(int r=(left+1); r < m; ++r) {
                       ~~^~~
fill_SMAWK.cpp: In function 'void fill_even_positions(int, int, int, int, const std::vector<unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)':
fill_SMAWK.cpp:164:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     for(++ r; r < n && js[r]<=jmax; r++) {
               ~~^~~
fill_SMAWK.cpp:164:29: warning: comparison of integer expressions of different signedness: 'const value_type' {aka 'const unsigned int'} and 'int' [-Wsign-compare]
     for(++ r; r < n && js[r]<=jmax; r++) {
fill_SMAWK.cpp:168:15: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare]
       if(jabs > i) break;
          ~~~~~^~~
fill_SMAWK.cpp: In function 'void find_min_from_candidates(int, int, int, int, const std::vector<unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)':
fill_SMAWK.cpp:218:16: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare]
       if(j_abs > i) break;
          ~~~~~~^~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getTautStringApprox.cpp -o getTautStringApprox.o
getTautStringApprox.cpp: In function 'Rcpp::List getTautStringApprox(std::vector<double>)':
getTautStringApprox.cpp:32:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (int i = 1; i != fullString.size(); ++i) {
                   ~~^~~~~~~~~~~~~~~~~~~~
getTautStringApprox.cpp:56:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<stringPairs>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (int i  = 0; i != plotSpecs.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kMedDP.cpp -o kMedDP.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kkuiper.cpp -o kkuiper.o
kkuiper.cpp: In function 'void difficultmax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:77:10: warning: variable 'min' set but not used [-Wunused-but-set-variable]
   double min, max;
          ^~~
kkuiper.cpp: In function 'void easymax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
     ~~~~~^~~~~
kkuiper.cpp: In function 'void difficultmax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:161:23: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
       *erga=minis[maxi];
                       ^
kkuiper.cpp: In function 'std::vector<double> kkuiper(std::vector<double>&, long int, int)':
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:44:15: note: 'maxi' was declared here
   long i,mini,maxi;
               ^~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
     ~~~~~^~~~~
kkuiper.cpp:44:10: note: 'mini' was declared here
   long i,mini,maxi;
          ^~~~
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:44:15: note: 'maxi' was declared here
   long i,mini,maxi;
               ^~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
     ~~~~~^~~~~
kkuiper.cpp:44:10: note: 'mini' was declared here
   long i,mini,maxi;
          ^~~~
kkuiper.cpp:58:3: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(mini<maxi) {
   ^~
kkuiper.cpp:44:15: note: 'maxi' was declared here
   long i,mini,maxi;
               ^~~~
kkuiper.cpp:58:3: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(mini<maxi) {
   ^~
kkuiper.cpp:44:10: note: 'mini' was declared here
   long i,mini,maxi;
          ^~~~
kkuiper.cpp:197:9: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     a[0]=maxi;
kkuiper.cpp:196:9: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     b[0]=mini;
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c local_density.cpp -o local_density.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c medianAbsoluteDeviation.cpp -o medianAbsoluteDeviation.o
medianAbsoluteDeviation.cpp: In function 'double medianAbsoluteDeviation(const std::vector<double>&)':
medianAbsoluteDeviation.cpp:28:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (auto i = 0; i != devs.size(); ++i)
                    ~~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c misc.cpp -o misc.o
misc.cpp: In function 'Rcpp::NumericMatrix collapseData(Rcpp::List, Rcpp::StringVector)':
misc.cpp:10:24: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
  for(unsigned i = 0; i < mat_list.size(); i++){
                      ~~^~~~~~~~~~~~~~~~~
misc.cpp:21:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for(unsigned ind = 0; ind < mat_list.size(); ind++){
                           ~~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rQuantile.cpp -o rQuantile.o
rQuantile.cpp: In function 'std::vector<double> rQuantile(const std::vector<double>&, std::vector<double>)':
rQuantile.cpp:35:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (auto i = 0; i != lowInd.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~
rQuantile.cpp:41:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (auto i = 0; i != lowInd.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~
rQuantile.cpp:47:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (auto i = 0; i != offSet.size(); ++i)
                    ~~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c singleDip.cpp -o singleDip.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tautstring.cpp -o tautstring.o
tautstring.cpp: In function 'stringInfo tautString(const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, double, double, long int, int)':
tautstring.cpp:148:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (auto i = 0; i < knotst.size(); i++) {
                    ~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tsGates.cpp -o tsGates.o
tsGates.cpp: In function 'std::vector<double> findKmedGates(const std::vector<double>&, const std::vector<int>&, int)':
tsGates.cpp:41:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for (auto j = 0; j != classVector.size(); j++)
                      ~~^~~~~~~~~~~~~~~~~~~~~
tsGates.cpp: In function 'std::vector<double> tsGates(const std::vector<double>&, int)':
tsGates.cpp:81:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for (auto i = 1; i != (localMins.size()-1); ++i) {
                      ~~^~~~~~~~~~~~~~~~~~~~~~~
tsGates.cpp:86:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for (auto i = 0; i != yvals.size(); ++i)
                      ~~^~~~~~~~~~~~~~~
tsGates.cpp:96:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for (auto j = 0; j != cutValues.size(); ++j) {
                      ~~^~~~~~~~~~~~~~~~~~~
tsGates.cpp:99:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for (auto i = 0; i != ys.size(); ++i)
                        ~~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c unlockNamespace.c -o unlockNamespace.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o openCyto.dll tmp.def RcppExports.o cpPmden.o cppApprox.o cppdip.o dynamic_prog.o fill_SMAWK.o getTautStringApprox.o kMedDP.o kkuiper.o local_density.o medianAbsoluteDeviation.o misc.o rQuantile.o singleDip.o tautstring.o tsGates.o unlockNamespace.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'openCyto'
    finding HTML links ... done
    CytoExploreR_exports                    html  
    add                                     html  
    as.data.table                           html  
    boolMethod-class                        html  
    dims-gtMethod-method                    html  
    dummyMethod-class                       html  
    fcEllipsoidGate-class                   html  
    fcEllipsoidGate                         html  
    fcFilter-class                          html  
    fcFilterList-class                      html  
    fcFilterList                            html  
    fcPolygonGate-class                     html  
    fcPolygonGate                           html  
    fcRectangleGate-class                   html  
    fcRectangleGate                         html  
    fcTree-class                            html  
    fcTree                                  html  
    gate_flowclust_1d                       html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/help/gate_flowClust_1d.html
    finding level-2 HTML links ... done

    gate_flowclust_2d                       html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/help/gate_flowClust_2d.html
    gate_mindensity                         html  
    gate_mindensity2                        html  
    gate_quad_sequential                    html  
    gate_quad_tmix                          html  
    gate_quantile                           html  
    gate_tail                               html  
    gate_tautstring                         html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/help/tautString.html
    gatingTemplate-class                    html  
    getGate-fcTree-character-method         html  
    getNodes-fcTree-method                  html  
    gh_generate_template                    html  
    groupBy-gtMethod-method                 html  
    gs_add_gating_method                    html  
    gs_add_gating_method_init               html  
    gs_remove_gating_method                 html  
    gtMethod-class                          html  
    gtPopulation-class                      html  
    gtSubsets-class                         html  
    gt_gating                               html  
    gt_get_children                         html  
    gt_get_gate                             html  
    gt_get_nodes                            html  
    gt_get_parent                           html  
    gt_list_methods                         html  
    gt_toggle_helpergates                   html  
    isCollapse-gtMethod-method              html  
    names-gtMethod-method                   html  
    names-gtPopulation-method               html  
    ocRectRefGate-class                     html  
    ocRectRefGate                           html  
    ocRectangleGate-class                   html  
    openCyto-deprecated                     html  
    openCyto                                html  
    openCyto.options                        html  
    parameters-gtMethod-method              html  
    plot-fcFilterList-ANY-method            html  
    plot-fcTree-character-method            html  
    plot-gatingTemplate-missing-method      html  
    polyFunctions-class                     html  
    posteriors-fcFilter-ANY-method          html  
    ppMethod-class                          html  
    ppMethod-gatingTemplate-character-method
                                            html  
    preprocessing-ppMethod-GatingSet-method
                                            html  
    prior_flowclust                         html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/help/prior_flowClust.html
    priors-fcFilter-ANY-method              html  
    refGate-class                           html  
    register_plugins                        html  
    show-boolMethod-method                  html  
    show-fcFilter-method                    html  
    show-gatingTemplate-method              html  
    show-gtMethod-method                    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

install for x64

* installing *source* package 'openCyto' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cpPmden.cpp -o cpPmden.o
cpPmden.cpp: In function 'stringInfo cpPmden(const std::vector<double>&)':
cpPmden.cpp:88:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
   for (auto i = 0; i < (nsamp-1); i++) {
                    ~~^~~~~~~~~~~
cpPmden.cpp:100:17: warning: variable 'newaccx' set but not used [-Wunused-but-set-variable]
     double rhs, newaccx;
                 ^~~~~~~
cpPmden.cpp:157:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     for (auto i = 0; i < nsamp; i++) {
                      ~~^~~~~~~
cpPmden.cpp:164:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     for (auto i=0; i < (nsamp-2); i++) {
                    ~~^~~~~~~~~~~
cpPmden.cpp:193:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     for (auto i = 0; i < nsamp; i++) {
                      ~~^~~~~~~
cpPmden.cpp:219:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
       for (auto i = 0; i < nsamp; i++) {
                        ~~^~~~~~~
cpPmden.cpp:251:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
       for (auto i = 0; i < nsamp; i++) {
                        ~~^~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cppApprox.cpp -o cppApprox.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cppdip.cpp -o cppdip.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dynamic_prog.cpp -o dynamic_prog.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fill_SMAWK.cpp -o fill_SMAWK.o
fill_SMAWK.cpp: In function 'void reduce_in_place(int, int, int, int, const std::vector<long long unsigned int>&, std::vector<long long unsigned int>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<long long unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)':
fill_SMAWK.cpp:80:8: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long long unsigned int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   if(N >= js.size()) {
      ~~^~~~~~~~~~~~
fill_SMAWK.cpp:90:11: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   while(m > N) { // js_reduced has more than N positions / columns
         ~~^~~
fill_SMAWK.cpp:121:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(int r=(left+1); r < m; ++r) {
                       ~~^~~
fill_SMAWK.cpp: In function 'void fill_even_positions(int, int, int, int, const std::vector<long long unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<long long unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)':
fill_SMAWK.cpp:164:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     for(++ r; r < n && js[r]<=jmax; r++) {
               ~~^~~
fill_SMAWK.cpp:164:29: warning: comparison of integer expressions of different signedness: 'const value_type' {aka 'const long long unsigned int'} and 'int' [-Wsign-compare]
     for(++ r; r < n && js[r]<=jmax; r++) {
fill_SMAWK.cpp:168:15: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'int' [-Wsign-compare]
       if(jabs > i) break;
          ~~~~~^~~
fill_SMAWK.cpp: In function 'void find_min_from_candidates(int, int, int, int, const std::vector<long long unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<long long unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)':
fill_SMAWK.cpp:218:16: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'int' [-Wsign-compare]
       if(j_abs > i) break;
          ~~~~~~^~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getTautStringApprox.cpp -o getTautStringApprox.o
getTautStringApprox.cpp: In function 'Rcpp::List getTautStringApprox(std::vector<double>)':
getTautStringApprox.cpp:32:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (int i = 1; i != fullString.size(); ++i) {
                   ~~^~~~~~~~~~~~~~~~~~~~
getTautStringApprox.cpp:56:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<stringPairs>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (int i  = 0; i != plotSpecs.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kMedDP.cpp -o kMedDP.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kkuiper.cpp -o kkuiper.o
kkuiper.cpp: In function 'void difficultmax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:77:10: warning: variable 'min' set but not used [-Wunused-but-set-variable]
   double min, max;
          ^~~
kkuiper.cpp: In function 'void easymax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
     ~~~~~^~~~~
kkuiper.cpp: In function 'void difficultmax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:161:23: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
       *erga=minis[maxi];
                       ^
kkuiper.cpp: In function 'std::vector<double> kkuiper(std::vector<double>&, long int, int)':
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:44:15: note: 'maxi' was declared here
   long i,mini,maxi;
               ^~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
     ~~~~~^~~~~
kkuiper.cpp:44:10: note: 'mini' was declared here
   long i,mini,maxi;
          ^~~~
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:44:15: note: 'maxi' was declared here
   long i,mini,maxi;
               ^~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
     ~~~~~^~~~~
kkuiper.cpp:44:10: note: 'mini' was declared here
   long i,mini,maxi;
          ^~~~
kkuiper.cpp:58:3: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(mini<maxi) {
   ^~
kkuiper.cpp:44:15: note: 'maxi' was declared here
   long i,mini,maxi;
               ^~~~
kkuiper.cpp:58:3: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(mini<maxi) {
   ^~
kkuiper.cpp:44:10: note: 'mini' was declared here
   long i,mini,maxi;
          ^~~~
kkuiper.cpp:197:9: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     a[0]=maxi;
kkuiper.cpp:196:9: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     b[0]=mini;
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c local_density.cpp -o local_density.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c medianAbsoluteDeviation.cpp -o medianAbsoluteDeviation.o
medianAbsoluteDeviation.cpp: In function 'double medianAbsoluteDeviation(const std::vector<double>&)':
medianAbsoluteDeviation.cpp:28:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (auto i = 0; i != devs.size(); ++i)
                    ~~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c misc.cpp -o misc.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rQuantile.cpp -o rQuantile.o
rQuantile.cpp: In function 'std::vector<double> rQuantile(const std::vector<double>&, std::vector<double>)':
rQuantile.cpp:35:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (auto i = 0; i != lowInd.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~
rQuantile.cpp:41:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (auto i = 0; i != lowInd.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~
rQuantile.cpp:47:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (auto i = 0; i != offSet.size(); ++i)
                    ~~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c singleDip.cpp -o singleDip.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tautstring.cpp -o tautstring.o
tautstring.cpp: In function 'stringInfo tautString(const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, double, double, long int, int)':
tautstring.cpp:148:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (auto i = 0; i < knotst.size(); i++) {
                    ~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tsGates.cpp -o tsGates.o
tsGates.cpp: In function 'std::vector<double> findKmedGates(const std::vector<double>&, const std::vector<int>&, int)':
tsGates.cpp:41:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (auto j = 0; j != classVector.size(); j++)
                      ~~^~~~~~~~~~~~~~~~~~~~~
tsGates.cpp: In function 'std::vector<double> tsGates(const std::vector<double>&, int)':
tsGates.cpp:81:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (auto i = 1; i != (localMins.size()-1); ++i) {
                      ~~^~~~~~~~~~~~~~~~~~~~~~~
tsGates.cpp:86:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (auto i = 0; i != yvals.size(); ++i)
                      ~~^~~~~~~~~~~~~~~
tsGates.cpp:96:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (auto j = 0; j != cutValues.size(); ++j) {
                      ~~^~~~~~~~~~~~~~~~~~~
tsGates.cpp:99:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
       for (auto i = 0; i != ys.size(); ++i)
                        ~~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c unlockNamespace.c -o unlockNamespace.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o openCyto.dll tmp.def RcppExports.o cpPmden.o cppApprox.o cppdip.o dynamic_prog.o fill_SMAWK.o getTautStringApprox.o kMedDP.o kkuiper.o local_density.o medianAbsoluteDeviation.o misc.o rQuantile.o singleDip.o tautstring.o tsGates.o unlockNamespace.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/openCyto/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'openCyto' as openCyto_2.6.0.zip
* DONE (openCyto)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'openCyto' successfully unpacked and MD5 sums checked