* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘sommer’ ...
** this is package ‘sommer’ version ‘4.4.2’
** package ‘sommer’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’
make[1]: Entering directory '/tmp/RtmpYRmwi4/R.INSTALL351fc6992da21/sommer/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c MNR.cpp -o MNR.o
MNR.cpp: In function ‘arma::cube scorecalc(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, int, double)’:
MNR.cpp:458:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  458 |     for (int i = 0; i < b.n_rows; ++i) {
      |                     ~~^~~~~~~~~~
MNR.cpp: In function ‘Rcpp::List newton_di_sp(const arma::sp_mat&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::sp_mat&, const bool&, int, double, double, const bool&, const bool&, const bool&, const bool&, const arma::vec&, const arma::vec&, const Rcpp::List&, const arma::vec&)’:
MNR.cpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  646 |     for(int h=0; h < provX.n_cols ; h++){ // for each random effect unlist
      |                  ~~^~~~~~~~~~~~~~
MNR.cpp:1144:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1144 |     for (int j = 0; j < thetaConstOriIth.n_cols; ++j) { // for each row in theta
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~
MNR.cpp:1145:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1145 |       for (int k = 0; k < thetaConstOriIth.n_rows; ++k) { // for each col in theta
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~
MNR.cpp:1158:36: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
 1158 |               if( blupTable.n_cols <= j){ // not yet populated
      |                   ~~~~~~~~~~~~~~~~~^~~~
MNR.cpp:1190:35: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
 1190 |               if(blupTable.n_cols <= j){ // not yet populated
      |                  ~~~~~~~~~~~~~~~~~^~~~
MNR.cpp:1201:36: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
 1201 |               if( blupTable.n_cols <= k){ // not yet populated
      |                   ~~~~~~~~~~~~~~~~~^~~~
MNR.cpp:1226:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1226 |       for (int l = 0; l < blupTable.n_cols; ++l) {
      |                       ~~^~~~~~~~~~~~~~~~~~
MNR.cpp:1247:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘long long unsigned int’} [-Wsign-compare]
 1247 |     for (int i = 0; i < partitions.size(); ++i) {//for each major random effect
      |                     ~~^~~~~~~~~~~~~~~~~~~
MNR.cpp: In function ‘Rcpp::List ai_mme_sp(const arma::sp_mat&, const Rcpp::List&, const arma::vec&, const Rcpp::List&, const arma::sp_mat&, const Rcpp::List&, const Rcpp::List&, const arma::sp_mat&, const bool&, int, double, double, double, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const arma::vec&, const arma::vec&, const arma::vec&, const bool&)’:
MNR.cpp:1725:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1725 |         for(int iRow = 0; iRow < partitionsP.n_rows; ++iRow){ // for each partition row
      |                           ~~~~~^~~~~~~~~~~~~~~~~~~~
MNR.cpp:1742:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1742 |         for(int iRow = 0; iRow < lambda(iR).n_rows; ++iRow){
      |                           ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1743:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1743 |           for(int iCol = 0; iCol < lambda(iR).n_cols; ++iCol){
      |                             ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1766:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘long long unsigned int’} [-Wsign-compare]
 1766 |     for(int iS = 0; iS < Si.size(); ++iS){
      |                     ~~~^~~~~~~~~~~
MNR.cpp:1856:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1856 |         for(int iRow = 0; iRow < lambda(iR).n_rows; ++iRow){
      |                           ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1857:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1857 |           for(int iCol = 0; iCol < lambda(iR).n_cols; ++iCol){
      |                             ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1883:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘long long unsigned int’} [-Wsign-compare]
 1883 |     for(int iS = 0; iS < Si.size(); ++iS){ // Rij <- S[[iS]]%*%Ri
      |                     ~~~^~~~~~~~~~~
MNR.cpp:1941:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘long long unsigned int’} [-Wsign-compare]
 1941 |     for(int i = 0; i < thetaCUnlisted.size() ; ++i){
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~
MNR.cpp:1948:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1948 |           for(int j = 0; j < toBoundary.n_cols ; ++j){
      |                          ~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:2125:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 2125 |     for (int j = 0; j < partitionsP.n_rows; ++j) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~
MNR.cpp:1393:10: warning: unused variable ‘vary2’ [-Wunused-variable]
 1393 |   double vary2 = arma::mean(arma::var(arma::square(y0)));
      |          ^~~~~
MNR.cpp: In function ‘Rcpp::List MNR(const arma::mat&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const bool&, int, double, double, const bool&, const bool&, const bool&, const bool&, const arma::vec&, const arma::vec&)’:
MNR.cpp:2285:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 2285 |     for(int h=0; h < provX.n_cols ; h++){ // for each random effect unlist
      |                  ~~^~~~~~~~~~~~~~
MNR.cpp: In function ‘arma::vec varCols(const arma::mat&)’:
MNR.cpp:149:19: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized]
  149 |     out(j) = M2/(n-1);
      |                 ~~^~~
MNR.cpp:139:9: note: ‘n’ was declared here
  139 |     int n;
      |         ^
MNR.cpp: In function ‘Rcpp::List newton_di_sp(const arma::sp_mat&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::sp_mat&, const bool&, int, double, double, const bool&, const bool&, const bool&, const bool&, const arma::vec&, const arma::vec&, const Rcpp::List&, const arma::vec&)’:
MNR.cpp:1124:48: warning: ‘cycle2’ may be used uninitialized [-Wmaybe-uninitialized]
 1124 |     sigma_perc_change2 = sigma_perc_change.cols(1, cycle2); // indicate first and last column to subset to return at the end
      |                          ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
MNR.cpp:731:14: note: ‘cycle2’ was declared here
  731 |   int cycle, cycle2, ikk;
      |              ^~~~~~
MNR.cpp:1112:20: warning: ‘llik’ may be used uninitialized [-Wmaybe-uninitialized]
 1112 |   double AIC = (-2 * llik) + (2 * Xm.n_cols);
      |                ~~~~^~~~~~~
MNR.cpp:732:16: note: ‘llik’ was declared here
  732 |   double ldet, llik, llik0, delta_llik, checkP, seconds; // to store likelihoods and determinants
      |                ^~~~
MNR.cpp: In function ‘Rcpp::List MNR(const arma::mat&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const bool&, int, double, double, const bool&, const bool&, const bool&, const bool&, const arma::vec&, const arma::vec&)’:
MNR.cpp:2758:36: warning: ‘cycle2’ may be used uninitialized [-Wmaybe-uninitialized]
 2758 |   arma::mat monitor2 = monitor.cols(0, cycle2);
      |                        ~~~~~~~~~~~~^~~~~~~~~~~
MNR.cpp:2369:14: note: ‘cycle2’ was declared here
 2369 |   int cycle, cycle2, ikk;
      |              ^~~~~~
MNR.cpp:2749:20: warning: ‘llik’ may be used uninitialized [-Wmaybe-uninitialized]
 2749 |   double AIC = (-2 * llik) + (2 * Xm.n_cols);
      |                ~~~~^~~~~~~
MNR.cpp:2370:16: note: ‘llik’ was declared here
 2370 |   double ldet, llik, llik0, delta_llik, checkP, seconds; // to store likelihoods and determinants
      |                ^~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o sommer.so MNR.o RcppExports.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpYRmwi4/R.INSTALL351fc6992da21/sommer/src'
make[1]: Entering directory '/tmp/RtmpYRmwi4/R.INSTALL351fc6992da21/sommer/src'
make[1]: Leaving directory '/tmp/RtmpYRmwi4/R.INSTALL351fc6992da21/sommer/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-sommer/00new/sommer/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sommer)