/usr/bin/tar: sommer/CHANGELOG: time stamp 2025-07-30 05:34:41 is 4759.0468758 s in the future /usr/bin/tar: sommer/DESCRIPTION: time stamp 2025-07-30 05:41:25 is 5163.0440425 s in the future /usr/bin/tar: sommer/R/FUN_methods_mmes.R: time stamp 2025-07-30 05:37:32 is 4930.037808 s in the future /usr/bin/tar: sommer/R/mmes.R: time stamp 2025-07-30 05:33:00 is 4658.0301929 s in the future /usr/bin/tar: sommer/R: time stamp 2025-07-30 05:41:24 is 5162.0275308 s in the future /usr/bin/tar: sommer/build/vignette.rds: time stamp 2025-07-30 05:41:24 is 5162.0255437 s in the future /usr/bin/tar: sommer/build: time stamp 2025-07-30 05:41:24 is 5162.0250692 s in the future /usr/bin/tar: sommer/data/DT_augment.RData: time stamp 2025-07-30 05:41:25 is 5163.0233825 s in the future /usr/bin/tar: sommer/data/DT_btdata.RData: time stamp 2025-07-30 05:41:25 is 5163.0218322 s in the future /usr/bin/tar: sommer/data/DT_cornhybrids.RData: time stamp 2025-07-30 05:41:25 is 5163.0209271 s in the future /usr/bin/tar: sommer/data/DT_cpdata.RData: time stamp 2025-07-30 05:41:26 is 5164.0191904 s in the future /usr/bin/tar: sommer/data/DT_example.RData: time stamp 2025-07-30 05:41:26 is 5164.0183134 s in the future /usr/bin/tar: sommer/data/DT_expdesigns.RData: time stamp 2025-07-30 05:41:26 is 5164.0173345 s in the future /usr/bin/tar: sommer/data/DT_fulldiallel.RData: time stamp 2025-07-30 05:41:26 is 5164.0166224 s in the future /usr/bin/tar: sommer/data/DT_gryphon.RData: time stamp 2025-07-30 05:41:27 is 5165.0155775 s in the future /usr/bin/tar: sommer/data/DT_h2.RData: time stamp 2025-07-30 05:41:27 is 5165.0146175 s in the future /usr/bin/tar: sommer/data/DT_halfdiallel.RData: time stamp 2025-07-30 05:41:27 is 5165.0138276 s in the future /usr/bin/tar: sommer/data/DT_ige.RData: time stamp 2025-07-30 05:41:27 is 5165.0124831 s in the future /usr/bin/tar: sommer/data/DT_legendre.RData: time stamp 2025-07-30 05:41:27 is 5165.0115067 s in the future /usr/bin/tar: sommer/data/DT_mohring.RData: time stamp 2025-07-30 05:41:27 is 5165.0107441 s in the future /usr/bin/tar: sommer/data/DT_polyploid.RData: time stamp 2025-07-30 05:41:30 is 5168.0085734 s in the future /usr/bin/tar: sommer/data/DT_rice.RData: time stamp 2025-07-30 05:41:30 is 5168.0073267 s in the future /usr/bin/tar: sommer/data/DT_sleepstudy.RData: time stamp 2025-07-30 05:41:30 is 5168.0062309 s in the future /usr/bin/tar: sommer/data/DT_technow.RData: time stamp 2025-07-30 05:41:36 is 5174.0029772 s in the future /usr/bin/tar: sommer/data/DT_wheat.RData: time stamp 2025-07-30 05:41:38 is 5176.0014605 s in the future /usr/bin/tar: sommer/data/DT_yatesoats.RData: time stamp 2025-07-30 05:41:38 is 5176.0006279 s in the future /usr/bin/tar: sommer/inst/doc/sommer.gxe.R: time stamp 2025-07-30 05:41:07 is 5144.9977877 s in the future /usr/bin/tar: sommer/inst/doc/sommer.gxe.html: time stamp 2025-07-30 05:41:07 is 5144.9955658 s in the future /usr/bin/tar: sommer/inst/doc/sommer.qg.R: time stamp 2025-07-30 05:41:17 is 5154.994828 s in the future /usr/bin/tar: sommer/inst/doc/sommer.qg.html: time stamp 2025-07-30 05:41:17 is 5154.9932366 s in the future /usr/bin/tar: sommer/inst/doc/sommer.spatial.R: time stamp 2025-07-30 05:41:22 is 5159.9924921 s in the future /usr/bin/tar: sommer/inst/doc/sommer.spatial.html: time stamp 2025-07-30 05:41:22 is 5159.9913269 s in the future /usr/bin/tar: sommer/inst/doc/sommer.vs.lme4.R: time stamp 2025-07-30 05:41:24 is 5161.9907945 s in the future /usr/bin/tar: sommer/inst/doc/sommer.vs.lme4.html: time stamp 2025-07-30 05:41:24 is 5161.9896827 s in the future /usr/bin/tar: sommer/inst/doc: time stamp 2025-07-30 05:41:24 is 5161.9894712 s in the future /usr/bin/tar: sommer/inst: time stamp 2025-07-30 05:41:24 is 5161.9893506 s in the future /usr/bin/tar: sommer/man: time stamp 2025-07-30 05:41:24 is 5161.931412 s in the future /usr/bin/tar: sommer/src: time stamp 2025-07-30 05:41:24 is 5161.9281238 s in the future /usr/bin/tar: sommer/tests: time stamp 2025-07-30 05:41:24 is 5161.9254224 s in the future /usr/bin/tar: sommer/vignettes: time stamp 2025-07-30 05:41:24 is 5161.90673 s in the future * installing *source* package 'sommer' ... ** this is package 'sommer' version '4.4.3' ** using staged installation ** libs using C++ compiler: 'g++.exe (GCC) 14.2.0' g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppProgress/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppProgress/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -shared -s -static-libgcc -o sommer.dll tmp.def MNR.o RcppExports.o -fopenmp -LD:/RCompile/recent/R/bin/x64 -lRlapack -LD:/RCompile/recent/R/bin/x64 -lRblas -lgfortran -lquadmath -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to d:/RCompile/CRANincoming/R-devel/lib/00LOCK-sommer/00new/sommer/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sommer)