* using log directory 'd:/Rcompile/CRANpkg/local/4.6/CytoSimplex.Rcheck'
* using R version 4.6.0 beta (2026-04-16 r89899 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* current time: 2026-04-17 08:10:00 UTC
* checking for file 'CytoSimplex/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CytoSimplex' version '0.2.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CytoSimplex' can be installed ... ERROR
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.6/CytoSimplex.Rcheck/00install.out' for details.
* DONE
The installation logfile:
* 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++.exe (GCC) 14.3.0'
make[1]: Entering directory '/d/temp/2026_04_17_01_50_00_1722/Rtmpo3QvUD/R.INSTALL99a02ef97567/CytoSimplex/src'
g++ -std=gnu++20  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"      -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c CytoSimplex.cpp -o CytoSimplex.o
In file included from D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/Rcpp.h:49,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:35,
                 from CytoSimplex.cpp:1:
D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/Rcpp/Function.h: In constructor 'Rcpp::Function_Impl<StoragePolicy>::Function_Impl(const std::string&, const std::string&)':
D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/Rcpp/Function.h:75:65: error: 'R_NamespaceRegistry' was not declared in this scope
   75 |             Shield<SEXP> env(R_getVarEx(Rf_install(ns.c_str()), R_NamespaceRegistry, FALSE, R_UnboundValue));
      |                                                                 ^~~~~~~~~~~~~~~~~~~
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 long unsigned int> >::size_type' {aka 'long 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 long unsigned int'} and 'int' [-Wsign-compare]
  201 |     for (size_t i = idx_begin; i <= idx_end; i++) {
      |                                ~~^~~~~~~~~~
make[1]: *** [D:/RCompile/recent/R/etc/x64/Makeconf:304: CytoSimplex.o] Error 1
make[1]: Leaving directory '/d/temp/2026_04_17_01_50_00_1722/Rtmpo3QvUD/R.INSTALL99a02ef97567/CytoSimplex/src'
ERROR: compilation failed for package 'CytoSimplex'
* removing 'd:/Rcompile/CRANpkg/lib/4.6/CytoSimplex'
* restoring previous 'd:/Rcompile/CRANpkg/lib/4.6/CytoSimplex'