* 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/RtmpZPuyRl/R.INSTALL983265adcb245/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/RtmpZPuyRl/R.INSTALL983265adcb245/sommer/src'
make[1]: Entering directory '/tmp/RtmpZPuyRl/R.INSTALL983265adcb245/sommer/src'
make[1]: Leaving directory '/tmp/RtmpZPuyRl/R.INSTALL983265adcb245/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)