* installing *source* package 'hibayes' ...
** package 'hibayes' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 12.3.0'
make[1]: Entering directory '/d/temp/Rtmp2xCWfx/R.INSTALL17ee8511c1a10/hibayes/src'
g++ -std=gnu++17  -I"D:/RCompile/recent/R-4.3.2/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/BH/include' -I'D:/RCompile/CRANpkg/lib/4.3/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.3/Matrix/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DARMA_64BIT_WORD=1 -fopenmp   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Bayes.cpp -o Bayes.o
Bayes.cpp: In function 'Rcpp::List makeZ(const Rcpp::CharacterVector&)':
Bayes.cpp:38:22: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   38 |     if (value.size() == n){
      |         ~~~~~~~~~~~~~^~~~
Bayes.cpp:45:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   45 |     for (int j = 0; j < value.size(); j++){
      |                     ~~^~~~~~~~~~~~~~
Bayes.cpp: In function 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)':
Bayes.cpp:103:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  103 |     for(int i = 0; i < Pi.n_elem; i++){
      |                    ~~^~~~~~~~~~~
Bayes.cpp:178:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  178 |         if(R_.nrow() != X.n_rows)   throw Rcpp::exception("Number of individuals does not match for environmental random effects.");
      |            ~~~~~~~~~~^~~~~~~~~~~
Bayes.cpp:405:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  405 |         for(int i = 0; i < Pi.n_elem; i++){
      |                        ~~^~~~~~~~~~~
Bayes.cpp:419:30: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  419 |             for(int i = 0; i < fold_.n_elem; i++){
      |                            ~~^~~~~~~~~~~~~~
Bayes.cpp:1008:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 1008 |             for(int j = 0; j < (Z_levels[i]).size(); j++){
      |                            ~~^~~~~~~~~~~~~~~~~~~~~~
Bayes.cpp:1045:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
 1045 |         for(int i = 0; i < Pi.n_elem; i++){
      |                        ~~^~~~~~~~~~~
Bayes.cpp:1054:22: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
 1054 |                 if(i != (Pi.n_elem - 1))  Rcpp::Rcout << ", ";
      |                    ~~^~~~~~~~~~~~~~~~~~
In file included from d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\iostream:39,
                 from D:/RCompile/CRANpkg/lib/4.3/Rcpp/include/RcppCommon.h:52,
                 from D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include/RcppArmadillo.h:29,
                 from hibayes.h:8,
                 from Bayes.cpp:1:
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
    inlined from 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)' at Bayes.cpp:1078:89:
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\ostream:221:25: warning: 'vepssd' may be used uninitialized [-Wmaybe-uninitialized]
  221 |       { return _M_insert(__f); }
      |                ~~~~~~~~~^~~~~
Bayes.cpp: In function 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)':
Bayes.cpp:238:12: note: 'vepssd' was declared here
  238 |     double vepssd;
      |            ^~~~~~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
    inlined from 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)' at Bayes.cpp:1074:150:
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\ostream:221:25: warning: 'vbsd' may be used uninitialized [-Wmaybe-uninitialized]
  221 |       { return _M_insert(__f); }
      |                ~~~~~~~~~^~~~~
Bayes.cpp: In function 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)':
Bayes.cpp:206:18: note: 'vbsd' was declared here
  206 |     double vasd, vbsd;
      |                  ^~~~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
    inlined from 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)' at Bayes.cpp:1074:88:
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\ostream:221:25: warning: 'vasd' may be used uninitialized [-Wmaybe-uninitialized]
  221 |       { return _M_insert(__f); }
      |                ~~~~~~~~~^~~~~
Bayes.cpp: In function 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)':
Bayes.cpp:206:12: note: 'vasd' was declared here
  206 |     double vasd, vbsd;
      |            ^~~~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
    inlined from 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)' at Bayes.cpp:1074:122:
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\ostream:221:25: warning: 'vb' may be used uninitialized [-Wmaybe-uninitialized]
  221 |       { return _M_insert(__f); }
      |                ~~~~~~~~~^~~~~
Bayes.cpp: In function 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)':
Bayes.cpp:204:16: note: 'vb' was declared here
  204 |     double va, vb;
      |                ^~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
    inlined from 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)' at Bayes.cpp:1074:60:
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\ostream:221:25: warning: 'va' may be used uninitialized [-Wmaybe-uninitialized]
  221 |       { return _M_insert(__f); }
      |                ~~~~~~~~~^~~~~
Bayes.cpp: In function 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)':
Bayes.cpp:204:12: note: 'va' was declared here
  204 |     double va, vb;
      |            ^~
Bayes.cpp:377:9: warning: 'nw' may be used uninitialized [-Wmaybe-uninitialized]
  377 |     int nw;
      |         ^~
Bayes.cpp:896:42: warning: 'NnzSnp' may be used uninitialized [-Wmaybe-uninitialized]
  896 |                 Rcpp::Rcout << NnzSnp << " ";
      |                                          ^~~
Bayes.cpp:281:9: note: 'NnzSnp' was declared here
  281 |     int NnzSnp, indistflag;
      |         ^~~~~~
Bayes.cpp:559:41: warning: 'JtJ' may be used uninitialized [-Wmaybe-uninitialized]
  559 |                         gi = norm_sample(rhs / v, sqrt(vare_ / v));
      |                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
Bayes.cpp:239:12: note: 'JtJ' was declared here
  239 |     double JtJ;
      |            ^~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R-4.3.2/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/BH/include' -I'D:/RCompile/CRANpkg/lib/4.3/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.3/Matrix/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DARMA_64BIT_WORD=1 -fopenmp   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R-4.3.2/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/BH/include' -I'D:/RCompile/CRANpkg/lib/4.3/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.3/Matrix/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DARMA_64BIT_WORD=1 -fopenmp   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SBayesD.cpp -o SBayesD.o
SBayesD.cpp: In function 'Rcpp::List SBayesD(arma::mat, arma::mat, std::string, arma::vec, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, int, int, bool)':
SBayesD.cpp:40:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
   40 |     for(int i = 0; i < Pi.n_elem; i++){
      |                    ~~^~~~~~~~~~~
SBayesD.cpp:197:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  197 |         for(int i = 0; i < Pi.n_elem; i++){
      |                        ~~^~~~~~~~~~~
SBayesD.cpp:211:30: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  211 |             for(int i = 0; i < fold_.n_elem; i++){
      |                            ~~^~~~~~~~~~~~~~
SBayesD.cpp:582:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  582 |         for(int i = 0; i < Pi.n_elem; i++){
      |                        ~~^~~~~~~~~~~
SBayesD.cpp:591:22: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  591 |                 if(i != (Pi.n_elem - 1))  Rcpp::Rcout << ", ";
      |                    ~~^~~~~~~~~~~~~~~~~~
SBayesD.cpp:174:9: warning: 'nw' may be used uninitialized [-Wmaybe-uninitialized]
  174 |     int nw;
      |         ^~
SBayesD.cpp:518:38: warning: 'NnzSnp' may be used uninitialized [-Wmaybe-uninitialized]
  518 |             Rcpp::Rcout << NnzSnp << " ";
      |                                      ^~~
SBayesD.cpp:61:9: note: 'NnzSnp' was declared here
   61 |     int NnzSnp, indistflag;
      |         ^~~~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R-4.3.2/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/BH/include' -I'D:/RCompile/CRANpkg/lib/4.3/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.3/Matrix/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DARMA_64BIT_WORD=1 -fopenmp   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SBayesS.cpp -o SBayesS.o
SBayesS.cpp: In function 'double spsubmatmtp(arma::sp_mat, arma::vec, arma::uvec)':
SBayesS.cpp:8:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
    8 |     for(int i = 0; i < windxi.n_elem; i++){
      |                    ~~^~~~~~~~~~~~~~~
SBayesS.cpp:10:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
   10 |         for(int j = 0; j < windxi.n_elem; j++){
      |                        ~~^~~~~~~~~~~~~~~
SBayesS.cpp: In function 'Rcpp::List SBayesS(arma::mat, arma::sp_mat, std::string, arma::vec, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, int, int, bool)':
SBayesS.cpp:56:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
   56 |     for(int i = 0; i < Pi.n_elem; i++){
      |                    ~~^~~~~~~~~~~
SBayesS.cpp:225:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  225 |         for(int i = 0; i < Pi.n_elem; i++){
      |                        ~~^~~~~~~~~~~
SBayesS.cpp:239:30: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  239 |             for(int i = 0; i < fold_.n_elem; i++){
      |                            ~~^~~~~~~~~~~~~~
SBayesS.cpp:652:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  652 |         for(int i = 0; i < Pi.n_elem; i++){
      |                        ~~^~~~~~~~~~~
SBayesS.cpp:661:22: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  661 |                 if(i != (Pi.n_elem - 1))  Rcpp::Rcout << ", ";
      |                    ~~^~~~~~~~~~~~~~~~~~
SBayesS.cpp:202:9: warning: 'nw' may be used uninitialized [-Wmaybe-uninitialized]
  202 |     int nw;
      |         ^~
SBayesS.cpp:588:38: warning: 'NnzSnp' may be used uninitialized [-Wmaybe-uninitialized]
  588 |             Rcpp::Rcout << NnzSnp << " ";
      |                                      ^~~
SBayesS.cpp:78:9: note: 'NnzSnp' was declared here
   78 |     int NnzSnp, indistflag;
      |         ^~~~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R-4.3.2/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/BH/include' -I'D:/RCompile/CRANpkg/lib/4.3/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.3/Matrix/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DARMA_64BIT_WORD=1 -fopenmp   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cg.cpp -o cg.o
cg.cpp: In function 'Rcpp::List conjgt_spa(Rcpp::NumericMatrix, arma::sp_mat, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, double, int, bool)':
cg.cpp:15:27: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
   15 |         if(sumstat.nrow() != ldm.n_rows){
      |            ~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cg.cpp: In function 'Rcpp::List conjgt_den(Rcpp::NumericMatrix, arma::mat, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, double, int, bool)':
cg.cpp:79:27: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
   79 |         if(sumstat.nrow() != ldm.n_rows){
      |            ~~~~~~~~~~~~~~~^~~~~~~~~~~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R-4.3.2/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/BH/include' -I'D:/RCompile/CRANpkg/lib/4.3/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.3/Matrix/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DARMA_64BIT_WORD=1 -fopenmp   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cutwind.cpp -o cutwind.o
cutwind.cpp: In function 'arma::vec cutwind_by_bp(const arma::vec&, const arma::vec&, double)':
cutwind.cpp:21:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
   21 |         for(int i = 0; i < unichr.n_elem; i++){
      |                        ~~^~~~~~~~~~~~~~~
cutwind.cpp: In function 'arma::vec cutwind_by_num(const arma::vec&, const arma::vec&, int)':
cutwind.cpp:45:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
   45 |         for(int i = 0; i < unichr.n_elem; i++){
      |                        ~~^~~~~~~~~~~~~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R-4.3.2/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/BH/include' -I'D:/RCompile/CRANpkg/lib/4.3/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.3/Matrix/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DARMA_64BIT_WORD=1 -fopenmp   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_bed.cpp -o read_bed.o
In file included from D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/shared_ptr.hpp:17,
                 from D:/RCompile/CRANpkg/lib/4.3/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from read_bed.cpp:4:
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\memory:75,
                 from D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
read_bed.cpp: In instantiation of 'void read_bed(std::string, Rcpp::XPtr<BigMatrix>, long int, double, bool, bool, int) [with T = char; std::string = std::__cxx11::basic_string<char>]':
read_bed.cpp:240:24:   required from here
read_bed.cpp:155:40: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  155 |                 for (size_t j = 0; j < cond; j++) {
      |                                        ^~~~
read_bed.cpp:160:54: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'index_type' {aka 'long long int'} [-Wsign-compare]
  160 |                         for (x = 0; x < 4 && (c + x) < pMat->nrow(); x++) {
      |                                              ~~~~~~~~^~~~~~~~~~~~~~
read_bed.cpp:218:46: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  218 |                                 if(counts[j] > max){
read_bed.cpp:142:16: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
  142 |         size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
      |                ^~~~~~~~~~~~
read_bed.cpp: In instantiation of 'void read_bed(std::string, Rcpp::XPtr<BigMatrix>, long int, double, bool, bool, int) [with T = short int; std::string = std::__cxx11::basic_string<char>]':
read_bed.cpp:242:25:   required from here
read_bed.cpp:155:40: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  155 |                 for (size_t j = 0; j < cond; j++) {
      |                                        ^~~~
read_bed.cpp:160:54: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'index_type' {aka 'long long int'} [-Wsign-compare]
  160 |                         for (x = 0; x < 4 && (c + x) < pMat->nrow(); x++) {
      |                                              ~~~~~~~~^~~~~~~~~~~~~~
read_bed.cpp:218:46: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  218 |                                 if(counts[j] > max){
read_bed.cpp:142:16: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
  142 |         size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
      |                ^~~~~~~~~~~~
read_bed.cpp: In instantiation of 'void read_bed(std::string, Rcpp::XPtr<BigMatrix>, long int, double, bool, bool, int) [with T = int; std::string = std::__cxx11::basic_string<char>]':
read_bed.cpp:244:23:   required from here
read_bed.cpp:155:40: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  155 |                 for (size_t j = 0; j < cond; j++) {
      |                                        ^~~~
read_bed.cpp:160:54: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'index_type' {aka 'long long int'} [-Wsign-compare]
  160 |                         for (x = 0; x < 4 && (c + x) < pMat->nrow(); x++) {
      |                                              ~~~~~~~~^~~~~~~~~~~~~~
read_bed.cpp:218:46: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  218 |                                 if(counts[j] > max){
read_bed.cpp:142:16: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
  142 |         size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
      |                ^~~~~~~~~~~~
read_bed.cpp: In instantiation of 'void read_bed(std::string, Rcpp::XPtr<BigMatrix>, long int, double, bool, bool, int) [with T = double; std::string = std::__cxx11::basic_string<char>]':
read_bed.cpp:246:26:   required from here
read_bed.cpp:155:40: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  155 |                 for (size_t j = 0; j < cond; j++) {
      |                                        ^~~~
read_bed.cpp:160:54: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'index_type' {aka 'long long int'} [-Wsign-compare]
  160 |                         for (x = 0; x < 4 && (c + x) < pMat->nrow(); x++) {
      |                                              ~~~~~~~~^~~~~~~~~~~~~~
read_bed.cpp:218:46: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  218 |                                 if(counts[j] > max){
read_bed.cpp:142:16: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
  142 |         size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
      |                ^~~~~~~~~~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R-4.3.2/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/BH/include' -I'D:/RCompile/CRANpkg/lib/4.3/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.3/Matrix/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DARMA_64BIT_WORD=1 -fopenmp   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rm.cpp -o rm.o
rm.cpp: In function 'SEXPREC* make_grm(arma::mat&, double, bool, bool, bool)':
rm.cpp:32:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   32 |     for (size_t j = 0; j < n; j++) {
      |                        ~~^~~
rm.cpp:33:44: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   33 |                 for (size_t i = (j + 1); i < n; i++) {
      |                                          ~~^~~
rm.cpp: In function 'Rcpp::List make_ped(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, bool)':
rm.cpp:68:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   68 |     for(int i = 0; i < pvec.size(); i++){
      |                    ~~^~~~~~~~~~~~~
rm.cpp:159:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  159 |     for (int j = 0; j < id.size(); j++){
      |                     ~~^~~~~~~~~~~
rm.cpp:163:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  163 |     for(int i = 0; i < id.size(); i++){
      |                    ~~^~~~~~~~~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R-4.3.2/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/BH/include' -I'D:/RCompile/CRANpkg/lib/4.3/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.3/Matrix/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DARMA_64BIT_WORD=1 -fopenmp   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c solver.cpp -o solver.o
solver.cpp: In function 'arma::vec PCGv(arma::mat, arma::vec, int, double)':
solver.cpp:6:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
    6 |         for(int i = 0; i < dA.n_elem; i++){
      |                        ~~^~~~~~~~~~~
solver.cpp: In function 'arma::vec CG(T, arma::vec, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, double, int, bool) [with T = arma::Mat<double>]':
solver.cpp:109:9: warning: 'err' may be used uninitialized [-Wmaybe-uninitialized]
  109 |         if(err < esp){
      |         ^~
solver.cpp:87:23: note: 'err' was declared here
   87 |         double alpha, err, beta;
      |                       ^~~
solver.cpp: In function 'arma::vec CG(T, arma::vec, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, double, int, bool) [with T = arma::SpMat<double>]':
solver.cpp:109:9: warning: 'err' may be used uninitialized [-Wmaybe-uninitialized]
  109 |         if(err < esp){
      |         ^~
solver.cpp:87:23: note: 'err' was declared here
   87 |         double alpha, err, beta;
      |                       ^~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R-4.3.2/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/BH/include' -I'D:/RCompile/CRANpkg/lib/4.3/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.3/Matrix/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DARMA_64BIT_WORD=1 -fopenmp   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stats.cpp -o stats.o
stats.cpp: In function 'Rcpp::IntegerVector which_c(Rcpp::NumericVector, double, int)':
stats.cpp:99:9: warning: 'logi' may be used uninitialized [-Wmaybe-uninitialized]
   99 |         if(logi){
      |         ^~
stats.cpp:82:10: note: 'logi' was declared here
   82 |     bool logi;
      |          ^~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R-4.3.2/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/BH/include' -I'D:/RCompile/CRANpkg/lib/4.3/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.3/Matrix/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DARMA_64BIT_WORD=1 -fopenmp   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tXXmat.cpp -o tXXmat.o
In file included from D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/shared_ptr.hpp:17,
                 from D:/RCompile/CRANpkg/lib/4.3/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from tXXmat.cpp:2:
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\memory:75,
                 from D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/RCompile/CRANpkg/lib/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = char; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
tXXmat.cpp:614:26:   required from here
tXXmat.cpp:530:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  530 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:537:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  537 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:543:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  543 |                                         for(i = j; i < chrindx.n_elem; i++){
      |                                                    ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:568:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  568 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:576:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  576 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:583:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  583 |                                         for(i = j + 1; i < chrindx.n_elem; i++){
      |                                                        ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:597:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  597 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:598:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  598 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = short int; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
tXXmat.cpp:616:27:   required from here
tXXmat.cpp:530:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  530 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:537:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  537 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:543:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  543 |                                         for(i = j; i < chrindx.n_elem; i++){
      |                                                    ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:568:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  568 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:576:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  576 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:583:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  583 |                                         for(i = j + 1; i < chrindx.n_elem; i++){
      |                                                        ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:597:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  597 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:598:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  598 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = int; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
tXXmat.cpp:618:25:   required from here
tXXmat.cpp:530:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  530 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:537:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  537 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:543:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  543 |                                         for(i = j; i < chrindx.n_elem; i++){
      |                                                    ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:568:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  568 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:576:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  576 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:583:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  583 |                                         for(i = j + 1; i < chrindx.n_elem; i++){
      |                                                        ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:597:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  597 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:598:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  598 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = float; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
tXXmat.cpp:620:27:   required from here
tXXmat.cpp:530:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  530 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:537:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  537 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:543:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  543 |                                         for(i = j; i < chrindx.n_elem; i++){
      |                                                    ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:568:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  568 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:576:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  576 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:583:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  583 |                                         for(i = j + 1; i < chrindx.n_elem; i++){
      |                                                        ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:597:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  597 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:598:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  598 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = double; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
tXXmat.cpp:622:28:   required from here
tXXmat.cpp:530:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  530 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:537:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  537 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:543:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  543 |                                         for(i = j; i < chrindx.n_elem; i++){
      |                                                    ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:568:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  568 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:576:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  576 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:583:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  583 |                                         for(i = j + 1; i < chrindx.n_elem; i++){
      |                                                        ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:597:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  597 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:598:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  598 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = char; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]':
tXXmat.cpp:828:31:   required from here
tXXmat.cpp:664:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  664 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:671:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  671 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:677:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  677 |                                         for(i = j; i < chrindx.n_elem; i++){
      |                                                    ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:709:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  709 |                                 for (j = 0; j < chrindx.n_elem; j++){
      |                                                         ^~~~~~
tXXmat.cpp:715:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  715 |                                                 for(i = j; i < chrindx.n_elem; i++){
      |                                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:741:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  741 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:749:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  749 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:756:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  756 |                                         for(i = j + 1; i < chrindx.n_elem; i++){
      |                                                        ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:774:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  774 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:775:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  775 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:787:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  787 |                                 for (j = 0; j < chrindx.n_elem; j++){
      |                                                         ^~~~~~
tXXmat.cpp:793:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  793 |                                                 for(i = j; i < chrindx.n_elem; i++){
      |                                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:810:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  810 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:811:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  811 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = short int; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]':
tXXmat.cpp:830:32:   required from here
tXXmat.cpp:664:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  664 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:671:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  671 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:677:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  677 |                                         for(i = j; i < chrindx.n_elem; i++){
      |                                                    ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:709:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  709 |                                 for (j = 0; j < chrindx.n_elem; j++){
      |                                                         ^~~~~~
tXXmat.cpp:715:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  715 |                                                 for(i = j; i < chrindx.n_elem; i++){
      |                                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:741:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  741 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:749:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  749 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:756:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  756 |                                         for(i = j + 1; i < chrindx.n_elem; i++){
      |                                                        ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:774:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  774 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:775:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  775 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:787:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  787 |                                 for (j = 0; j < chrindx.n_elem; j++){
      |                                                         ^~~~~~
tXXmat.cpp:793:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  793 |                                                 for(i = j; i < chrindx.n_elem; i++){
      |                                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:810:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  810 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:811:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  811 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = int; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]':
tXXmat.cpp:832:30:   required from here
tXXmat.cpp:664:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  664 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:671:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  671 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:677:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  677 |                                         for(i = j; i < chrindx.n_elem; i++){
      |                                                    ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:709:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  709 |                                 for (j = 0; j < chrindx.n_elem; j++){
      |                                                         ^~~~~~
tXXmat.cpp:715:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  715 |                                                 for(i = j; i < chrindx.n_elem; i++){
      |                                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:741:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  741 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:749:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  749 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:756:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  756 |                                         for(i = j + 1; i < chrindx.n_elem; i++){
      |                                                        ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:774:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  774 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:775:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  775 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:787:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  787 |                                 for (j = 0; j < chrindx.n_elem; j++){
      |                                                         ^~~~~~
tXXmat.cpp:793:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  793 |                                                 for(i = j; i < chrindx.n_elem; i++){
      |                                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:810:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  810 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:811:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  811 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = float; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]':
tXXmat.cpp:834:32:   required from here
tXXmat.cpp:664:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  664 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:671:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  671 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:677:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  677 |                                         for(i = j; i < chrindx.n_elem; i++){
      |                                                    ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:709:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  709 |                                 for (j = 0; j < chrindx.n_elem; j++){
      |                                                         ^~~~~~
tXXmat.cpp:715:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  715 |                                                 for(i = j; i < chrindx.n_elem; i++){
      |                                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:741:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  741 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:749:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  749 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:756:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  756 |                                         for(i = j + 1; i < chrindx.n_elem; i++){
      |                                                        ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:774:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  774 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:775:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  775 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:787:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  787 |                                 for (j = 0; j < chrindx.n_elem; j++){
      |                                                         ^~~~~~
tXXmat.cpp:793:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  793 |                                                 for(i = j; i < chrindx.n_elem; i++){
      |                                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:810:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  810 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:811:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  811 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = double; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]':
tXXmat.cpp:836:33:   required from here
tXXmat.cpp:664:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  664 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:671:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  671 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:677:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  677 |                                         for(i = j; i < chrindx.n_elem; i++){
      |                                                    ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:709:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  709 |                                 for (j = 0; j < chrindx.n_elem; j++){
      |                                                         ^~~~~~
tXXmat.cpp:715:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  715 |                                                 for(i = j; i < chrindx.n_elem; i++){
      |                                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:741:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  741 |                 for(int cc = 0; cc < unichr.n_elem; cc++){
      |                                 ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:749:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  749 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                                 ^~~~~~
tXXmat.cpp:756:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  756 |                                         for(i = j + 1; i < chrindx.n_elem; i++){
      |                                                        ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:774:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  774 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:775:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  775 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:787:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  787 |                                 for (j = 0; j < chrindx.n_elem; j++){
      |                                                         ^~~~~~
tXXmat.cpp:793:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  793 |                                                 for(i = j; i < chrindx.n_elem; i++){
      |                                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:810:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  810 |                         for (j = 0; j < chrindx.n_elem; j++){
      |                                     ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:811:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
  811 |                                 for(i = j; i < chrindx.n_elem; i++){
      |                                            ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = short int]':
tXXmat.cpp:536:33: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
  536 |                         #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
      |                                 ^~~
tXXmat.cpp:515:52: note: 'chisq_' was declared here
  515 |         double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
      |                                                    ^~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = double]':
tXXmat.cpp:536:33: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
  536 |                         #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
      |                                 ^~~
tXXmat.cpp:515:52: note: 'chisq_' was declared here
  515 |         double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
      |                                                    ^~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = char]':
tXXmat.cpp:536:33: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
  536 |                         #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
      |                                 ^~~
tXXmat.cpp:515:52: note: 'chisq_' was declared here
  515 |         double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
      |                                                    ^~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = float]':
tXXmat.cpp:536:33: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
  536 |                         #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
      |                                 ^~~
tXXmat.cpp:515:52: note: 'chisq_' was declared here
  515 |         double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
      |                                                    ^~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = int]':
tXXmat.cpp:536:33: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
  536 |                         #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
      |                                 ^~~
tXXmat.cpp:515:52: note: 'chisq_' was declared here
  515 |         double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
      |                                                    ^~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = double]':
tXXmat.cpp:708:41: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
  708 |                                 #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
      |                                         ^~~
tXXmat.cpp:643:52: note: 'chisq_' was declared here
  643 |         double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
      |                                                    ^~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = int]':
tXXmat.cpp:708:41: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
  708 |                                 #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
      |                                         ^~~
tXXmat.cpp:643:52: note: 'chisq_' was declared here
  643 |         double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
      |                                                    ^~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = short int]':
tXXmat.cpp:708:41: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
  708 |                                 #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
      |                                         ^~~
tXXmat.cpp:643:52: note: 'chisq_' was declared here
  643 |         double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
      |                                                    ^~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = float]':
tXXmat.cpp:708:41: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
  708 |                                 #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
      |                                         ^~~
tXXmat.cpp:643:52: note: 'chisq_' was declared here
  643 |         double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
      |                                                    ^~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = char]':
tXXmat.cpp:708:41: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
  708 |                                 #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
      |                                         ^~~
tXXmat.cpp:643:52: note: 'chisq_' was declared here
  643 |         double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
      |                                                    ^~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o hibayes.dll tmp.def Bayes.o RcppExports.o SBayesD.o SBayesS.o cg.o cutwind.o read_bed.o rm.o solver.o stats.o tXXmat.o -fopenmp -LD:/RCompile/recent/R-4.3.2/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.3.2/bin/x64 -lRblas -lgfortran -lm -lquadmath -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.3.2/bin/x64 -lR
make[1]: Leaving directory '/d/temp/Rtmp2xCWfx/R.INSTALL17ee8511c1a10/hibayes/src'
make[1]: Entering directory '/d/temp/Rtmp2xCWfx/R.INSTALL17ee8511c1a10/hibayes/src'
make[1]: Leaving directory '/d/temp/Rtmp2xCWfx/R.INSTALL17ee8511c1a10/hibayes/src'
installing to d:/Rcompile/CRANpkg/lib/4.3/00LOCK-hibayes/00new/hibayes/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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
* MD5 sums
packaged installation of 'hibayes' as hibayes_3.0.3.zip
* DONE (hibayes)