/usr/bin/tar: sommer/DESCRIPTION: time stamp 2025-02-03 19:36:10 is 7247.6313999 s in the future /usr/bin/tar: sommer/R/FUN_utils.R: time stamp 2025-02-03 19:34:51 is 7168.6195716 s in the future /usr/bin/tar: sommer/R/mmec.R: time stamp 2025-02-03 19:34:34 is 7151.615633 s in the future /usr/bin/tar: sommer/R/mmer.R: time stamp 2025-02-03 19:34:29 is 7146.6146511 s in the future /usr/bin/tar: sommer/R: time stamp 2025-02-03 19:36:10 is 7247.6123273 s in the future /usr/bin/tar: sommer/build/vignette.rds: time stamp 2025-02-03 19:36:10 is 7247.6106344 s in the future /usr/bin/tar: sommer/build: time stamp 2025-02-03 19:36:10 is 7247.6102949 s in the future /usr/bin/tar: sommer/data/DT_augment.RData: time stamp 2025-02-03 19:36:10 is 7247.6090906 s in the future /usr/bin/tar: sommer/data/DT_btdata.RData: time stamp 2025-02-03 19:36:10 is 7247.6079061 s in the future /usr/bin/tar: sommer/data/DT_cornhybrids.RData: time stamp 2025-02-03 19:36:10 is 7247.606804 s in the future 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sommer/inst/doc/v3.sommer.qg.R: time stamp 2025-02-03 19:35:50 is 7227.5765823 s in the future /usr/bin/tar: sommer/inst/doc/v4.sommer.gxe.R: time stamp 2025-02-03 19:36:06 is 7243.5715263 s in the future /usr/bin/tar: sommer/inst/doc/v5.sommer.vs.lme4.R: time stamp 2025-02-03 19:36:09 is 7246.5691532 s in the future /usr/bin/tar: sommer/inst/doc/v6.sommer.spatial.R: time stamp 2025-02-03 19:36:09 is 7246.567212 s in the future /usr/bin/tar: sommer/inst/doc: time stamp 2025-02-03 19:36:10 is 7247.5652445 s in the future /usr/bin/tar: sommer/inst: time stamp 2025-02-03 19:36:10 is 7247.5650687 s in the future /usr/bin/tar: sommer/man: time stamp 2025-02-03 19:36:10 is 7247.4970616 s in the future /usr/bin/tar: sommer/src: time stamp 2025-02-03 19:36:10 is 7247.4937471 s in the future /usr/bin/tar: sommer/tests: time stamp 2025-02-03 19:36:10 is 7247.4912987 s in the future /usr/bin/tar: sommer/vignettes/v1.sommer.quick.start.html: time stamp 2025-02-03 19:35:31 is 7208.4886672 s in the future /usr/bin/tar: sommer/vignettes/v2.sommer.changes.and.faqs.html: time stamp 2025-02-03 19:35:41 is 7218.4871525 s in the future /usr/bin/tar: sommer/vignettes/v3.sommer.qg.html: time stamp 2025-02-03 19:35:51 is 7228.4843817 s in the future /usr/bin/tar: sommer/vignettes/v4.sommer.gxe.html: time stamp 2025-02-03 19:36:07 is 7244.4822061 s in the future /usr/bin/tar: sommer/vignettes/v5.sommer.vs.lme4.html: time stamp 2025-02-03 19:36:09 is 7246.4808213 s in the future /usr/bin/tar: sommer/vignettes/v6.sommer.spatial.html: time stamp 2025-02-03 19:36:09 is 7246.4795068 s in the future /usr/bin/tar: sommer/vignettes: time stamp 2025-02-03 19:36:10 is 7247.4650102 s in the future * installing *source* package 'sommer' ... ** this is package 'sommer' version '4.3.7' ** using staged installation ** libs using C++ compiler: 'g++.exe (GCC) 13.3.0' g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c MNR.cpp -o MNR.o 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::cube scorecalc(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, int, double)': MNR.cpp:457:23: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 457 | 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:642:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 642 | 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:1306:12: warning: unused variable 'ok' [-Wunused-variable] 1306 | bool ok = log_det(val, sign, arma::mat(Ai[i])); // calculate the logDet of the covariance matrix | ^~ MNR.cpp:1529:14: warning: unused variable 'ok' [-Wunused-variable] 1529 | bool ok = log_det(val, sign, theta(i)); // form 2 | ^~ MNR.cpp:1577:32: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1577 | for(int iRow = 0; iRow < partitionsP.n_rows; ++iRow){ // for each partition row | ~~~~~^~~~~~~~~~~~~~~~~~~~ MNR.cpp:1595:32: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1595 | for(int iRow = 0; iRow < lambdaProv.n_rows; ++iRow){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1596:34: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1596 | for(int iCol = 0; iCol < lambdaProv.n_cols; ++iCol){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1621:24: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'unsigned int'} [-Wsign-compare] 1621 | for(int iS = 0; iS < S.size(); ++iS){ | ~~~^~~~~~~~~~ MNR.cpp:1702:32: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1702 | for(int iRow = 0; iRow < lambdaProv.n_rows; ++iRow){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1703:34: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1703 | for(int iCol = 0; iCol < lambdaProv.n_cols; ++iCol){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1729:24: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'unsigned int'} [-Wsign-compare] 1729 | for(int iS = 0; iS < S.size(); ++iS){ // Rij <- S[[iS]]%*%Ri | ~~~^~~~~~~~~~ MNR.cpp:1787:22: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'unsigned int'} [-Wsign-compare] 1787 | for(int i = 0; i < thetaCUnlisted.size() ; ++i){ | ~~^~~~~~~~~~~~~~~~~~~~~~~ MNR.cpp:1794:28: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1794 | for(int j = 0; j < toBoundary.n_cols ; ++j){ | ~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1535:10: warning: unused variable 'ok' [-Wunused-variable] 1535 | 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 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:1115:36: warning: 'cycle2' may be used uninitialized [-Wmaybe-uninitialized] 1115 | arma::mat monitor2 = monitor.cols(0, cycle2); | ~~~~~~~~~~~~^~~~~~~~~~~ MNR.cpp:726:14: note: 'cycle2' was declared here 726 | int cycle, cycle2, ikk; | ^~~~~~ MNR.cpp:1106:20: warning: 'llik' may be used uninitialized [-Wmaybe-uninitialized] 1106 | double AIC = (-2 * llik) + (2 * Xm.n_cols); | ~~~~^~~~~~~ MNR.cpp:727:16: note: 'llik' was declared here 727 | 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:1293:37: warning: 'nRe' may be used uninitialized [-Wmaybe-uninitialized] 1293 | arma::field Ai(nReAl); // allocate size of Ai field | ^ MNR.cpp:1252:7: note: 'nRe' was declared here 1252 | int nRe; | ^~~ g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/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 ** 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)