* installing *source* package ‘sommer’ ... ** this is package ‘sommer’ version ‘4.4.1’ ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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::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:655:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 655 | for(int h=0; h < provX.n_cols ; h++){ // for each random effect unlist | ~~^~~~~~~~~~~~~~ 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:1615:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1615 | for(int iRow = 0; iRow < partitionsP.n_rows; ++iRow){ // for each partition row | ~~~~~^~~~~~~~~~~~~~~~~~~~ MNR.cpp:1633:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1633 | for(int iRow = 0; iRow < lambdaProv.n_rows; ++iRow){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1634:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1634 | for(int iCol = 0; iCol < lambdaProv.n_cols; ++iCol){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1659:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘long long unsigned int’} [-Wsign-compare] 1659 | for(int iS = 0; iS < S.size(); ++iS){ | ~~~^~~~~~~~~~ MNR.cpp:1740:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1740 | for(int iRow = 0; iRow < lambdaProv.n_rows; ++iRow){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1741:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1741 | for(int iCol = 0; iCol < lambdaProv.n_cols; ++iCol){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1767:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘long long unsigned int’} [-Wsign-compare] 1767 | for(int iS = 0; iS < S.size(); ++iS){ // Rij <- S[[iS]]%*%Ri | ~~~^~~~~~~~~~ MNR.cpp:1825:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘long long unsigned int’} [-Wsign-compare] 1825 | for(int i = 0; i < thetaCUnlisted.size() ; ++i){ | ~~^~~~~~~~~~~~~~~~~~~~~~~ MNR.cpp:1832:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1832 | for(int j = 0; j < toBoundary.n_cols ; ++j){ | ~~^~~~~~~~~~~~~~~~~~~ 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:2126:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 2126 | 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 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:2599:36: warning: ‘cycle2’ may be used uninitialized [-Wmaybe-uninitialized] 2599 | arma::mat monitor2 = monitor.cols(0, cycle2); | ~~~~~~~~~~~~^~~~~~~~~~~ MNR.cpp:2210:14: note: ‘cycle2’ was declared here 2210 | int cycle, cycle2, ikk; | ^~~~~~ MNR.cpp:2590:20: warning: ‘llik’ may be used uninitialized [-Wmaybe-uninitialized] 2590 | double AIC = (-2 * llik) + (2 * Xm.n_cols); | ~~~~^~~~~~~ MNR.cpp:2211:16: note: ‘llik’ was declared here 2211 | double ldet, llik, llik0, delta_llik, checkP, seconds; // to store likelihoods and determinants | ^~~~ MNR.cpp: In function ‘Rcpp::List newton_di_sp(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:1143:48: warning: ‘cycle2’ may be used uninitialized [-Wmaybe-uninitialized] 1143 | sigma_perc_change2 = sigma_perc_change.cols(1, cycle2); // indicate first and last column to subset to return at the end | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ MNR.cpp:740:14: note: ‘cycle2’ was declared here 740 | int cycle, cycle2, ikk; | ^~~~~~ MNR.cpp:1131:20: warning: ‘llik’ may be used uninitialized [-Wmaybe-uninitialized] 1131 | double AIC = (-2 * llik) + (2 * Xm.n_cols); | ~~~~^~~~~~~ MNR.cpp:741:16: note: ‘llik’ was declared here 741 | double ldet, llik, llik0, delta_llik, checkP, seconds; // to store likelihoods and determinants | ^~~~ 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:1327:37: warning: ‘nRe’ may be used uninitialized [-Wmaybe-uninitialized] 1327 | arma::field Ai(nReAl); // allocate size of Ai field | ^ MNR.cpp:1286:7: note: ‘nRe’ was declared here 1286 | int nRe; | ^~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-gcc-14/lib -Wl,-O1 -o sommer.so MNR.o RcppExports.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR installing to /home/hornik/tmp/CRAN_recheck/sommer.Rcheck/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)