* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’ * installing *source* package ‘sommer’ ... ** package ‘sommer’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpcoMLql/R.INSTALL16416839ce4afc/sommer/src' g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -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 In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:26, from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29, from MNR.cpp:5: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: ‘#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed’ 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: ‘#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead’ 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: ‘#pragma message: INFO: see the documentation for details’ 329 | #pragma message ("INFO: see the documentation for details") | ^ MNR.cpp: In function ‘arma::mat dmat(const arma::mat&, const bool&, double)’: MNR.cpp:306:7: warning: unused variable ‘p’ [-Wunused-variable] 306 | int p = X.n_cols; | ^ MNR.cpp: In function ‘arma::rowvec scorecalc(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, int, double)’: MNR.cpp:453:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 453 | for (int i = 0; i < b.n_rows; ++i) { | ~~^~~~~~~~~~ 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:635:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 635 | 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:1299:12: warning: unused variable ‘ok’ [-Wunused-variable] 1299 | bool ok = log_det(val, sign, arma::mat(Ai[i])); // calculate the logDet of the covariance matrix | ^~ MNR.cpp:1522:14: warning: unused variable ‘ok’ [-Wunused-variable] 1522 | bool ok = log_det(val, sign, theta(i)); // form 2 | ^~ MNR.cpp:1570:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 1570 | for(int iRow = 0; iRow < partitionsP.n_rows; ++iRow){ // for each partition row | ~~~~~^~~~~~~~~~~~~~~~~~~~ MNR.cpp:1588:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 1588 | for(int iRow = 0; iRow < lambdaProv.n_rows; ++iRow){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1589:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 1589 | for(int iCol = 0; iCol < lambdaProv.n_cols; ++iCol){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1614:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare] 1614 | for(int iS = 0; iS < S.size(); ++iS){ | ~~~^~~~~~~~~~ MNR.cpp:1695:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 1695 | for(int iRow = 0; iRow < lambdaProv.n_rows; ++iRow){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1696:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 1696 | for(int iCol = 0; iCol < lambdaProv.n_cols; ++iCol){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1722:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare] 1722 | for(int iS = 0; iS < S.size(); ++iS){ // Rij <- S[[iS]]%*%Ri | ~~~^~~~~~~~~~ MNR.cpp:1780:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare] 1780 | for(int i = 0; i < thetaCUnlisted.size() ; ++i){ | ~~^~~~~~~~~~~~~~~~~~~~~~~ MNR.cpp:1787:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 1787 | for(int j = 0; j < toBoundary.n_cols ; ++j){ | ~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1528:10: warning: unused variable ‘ok’ [-Wunused-variable] 1528 | bool ok = log_det(val, sign, theta(nRRe-1)); // form 2 | ^~ MNR.cpp: In function ‘arma::vec varCols(const arma::mat&)’: MNR.cpp:148:19: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized] 148 | out(j) = M2/(n-1); | ~~^~~ MNR.cpp:138:9: note: ‘n’ was declared here 138 | int n; | ^ 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:1286:37: warning: ‘nRe’ may be used uninitialized [-Wmaybe-uninitialized] 1286 | arma::field Ai(nReAl); // allocate size of Ai field | ^ MNR.cpp:1245:7: note: ‘nRe’ was declared here 1245 | int nRe; | ^~~ 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:1108:36: warning: ‘cycle2’ may be used uninitialized [-Wmaybe-uninitialized] 1108 | arma::mat monitor2 = monitor.cols(0, cycle2); | ~~~~~~~~~~~~^~~~~~~~~~~ MNR.cpp:719:14: note: ‘cycle2’ was declared here 719 | int cycle, cycle2, ikk; | ^~~~~~ MNR.cpp:1099:20: warning: ‘llik’ may be used uninitialized [-Wmaybe-uninitialized] 1099 | double AIC = (-2 * llik) + (2 * Xm.n_cols); | ~~~~^~~~~~~ MNR.cpp:720:16: note: ‘llik’ was declared here 720 | double ldet, llik, llik0, delta_llik, checkP, seconds; // to store likelihoods and determinants | ^~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -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++-13 -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 '/home/hornik/tmp/scratch/RtmpcoMLql/R.INSTALL16416839ce4afc/sommer/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpcoMLql/R.INSTALL16416839ce4afc/sommer/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpcoMLql/R.INSTALL16416839ce4afc/sommer/src' installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-sommer/00new/sommer/libs ** R ** data ** 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 * creating tarball packaged installation of ‘sommer’ as ‘sommer_4.3.4_R_x86_64-pc-linux-gnu.tar.gz’ * DONE (sommer)