* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘CytoSimplex’ ...
** this is package ‘CytoSimplex’ version ‘0.2.0’
** package ‘CytoSimplex’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpWASWmG/R.INSTALL1b73ca7e87f3db/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/RtmpWASWmG/R.INSTALL1b73ca7e87f3db/CytoSimplex/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpWASWmG/R.INSTALL1b73ca7e87f3db/CytoSimplex/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpWASWmG/R.INSTALL1b73ca7e87f3db/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  
    plotQuaternary.Seurat                   html  
    plotQuaternary.SingleCellExperiment     html  
    plotQuaternary.simMat                   html  
    plotTernary                             html  
    plotTernary.Seurat                      html  
    plotTernary.SingleCellExperiment        html  
    plotTernary.simMat                      html  
    print-quatPlot                          html  
    readH5ADObsNames                        html  
    readH5ADObsVar                          html  
    readH5ADUnsSpMat                        html  
    readVelocytoLoom                        html  
    rnaCluster                              html  
    rnaRaw                                  html  
    rnaVelo                                 html  
    selectTopFeatures                       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)