* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘CytoSimplex’ ...
** package ‘CytoSimplex’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpq8zrqI/R.INSTALL2eb10678f296df/CytoSimplex/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c CytoSimplex.cpp -o CytoSimplex.o
CytoSimplex.cpp: In function ‘Rcpp::List rankMatrix_dense(arma::mat&)’:
CytoSimplex.cpp:175:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<float, long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  175 |         for (int i = 1; i < v_sort.size(); i++) {
      |                         ~~^~~~~~~~~~~~~~~
CytoSimplex.cpp:178:51: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  178 |                 for (unsigned j = tieStartRank; j < i; j++) {
      |                                                 ~~^~~
CytoSimplex.cpp: In function ‘std::__cxx11::list<float> cpp_in_place_rank_mean(arma::vec&, int, int)’:
CytoSimplex.cpp:201:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  201 |     for (size_t i = idx_begin; i <= idx_end; i++) {
      |                                ~~^~~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o CytoSimplex.so CytoSimplex.o RcppExports.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpq8zrqI/R.INSTALL2eb10678f296df/CytoSimplex/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpq8zrqI/R.INSTALL2eb10678f296df/CytoSimplex/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpq8zrqI/R.INSTALL2eb10678f296df/CytoSimplex/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-CytoSimplex/00new/CytoSimplex/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘CytoSimplex’
    finding HTML links ... done
    colNormalize                            html  
    plotBinary                              html  
    plotQuaternary                          html  
    plotTernary                             html  
    rnaCluster                              html  
    rnaRaw                                  html  
    rnaVelo                                 html  
    selectTopFeatures                       html  
    show-plist                              html  
    writeQuaternaryGIF                      html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CytoSimplex)