############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL miloR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘miloR’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c computeMatrices.cpp -o computeMatrices.o computeMatrices.cpp: In function ‘arma::mat initialiseG(Rcpp::List, arma::vec)’: computeMatrices.cpp:135:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 135 | for(unsigned long k=0; k < stot; k++){ | ~~^~~~~~ computeMatrices.cpp:143:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 143 | for(int l=0; l < q; l++){ | ~~^~~ computeMatrices.cpp: In function ‘arma::mat invGmat(Rcpp::List, arma::vec)’: computeMatrices.cpp:327:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 327 | for(unsigned long k=0; k < stot; k++){ | ~~^~~~~~ computeMatrices.cpp:335:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 335 | for(int l=0; l < q; l++){ | ~~^~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o fitGeneticPLGlmm.cpp: In function ‘Rcpp::List fitGeneticPLGlmm(const mat&, const mat&, const mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const vec&, Rcpp::List, double, const List&, double, const bool&, const int&, std::string, std::string)’: fitGeneticPLGlmm.cpp:197:10: warning: unused variable ‘_phi_est’ [-Wunused-variable] 197 | bool _phi_est = true; // control if we re-estimate phi or not | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c fitPLGlmm.cpp -o fitPLGlmm.o fitPLGlmm.cpp: In function ‘Rcpp::List fitPLGlmm(const mat&, const mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const vec&, Rcpp::List, double, const List&, double, const bool&, const int&, std::string, std::string)’: fitPLGlmm.cpp:177:10: warning: unused variable ‘_phi_est’ [-Wunused-variable] 177 | bool _phi_est = true; // control if we re-estimate phi or not | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c inference.cpp -o inference.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c invertPseudoVar.cpp -o invertPseudoVar.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c multiP.cpp -o multiP.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c paramEst.cpp -o paramEst.o paramEst.cpp: In function ‘arma::vec sigmaScoreREML_arma(const List&, const vec&, const mat&, const vec&, const mat&, const mat&)’: paramEst.cpp:29:33: warning: left operand of comma operator has no effect [-Wunused-value] 29 | double rhs = 0.5 * mid1[0, 0]; | ^ paramEst.cpp: In function ‘arma::vec estHasemanElstonGenetic(const mat&, const mat&, const List&, const vec&, const mat&)’: paramEst.cpp:258:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 258 | for (int i = 0; i < n; i++) { | ~~^~~ paramEst.cpp:259:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 259 | for (int j = i; j < n; j++) { | ~~^~~ paramEst.cpp:252:18: warning: unused variable ‘i’ [-Wunused-variable] 252 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:252:21: warning: unused variable ‘j’ [-Wunused-variable] 252 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:253:12: warning: unused variable ‘_ycovij’ [-Wunused-variable] 253 | double _ycovij; // Declare temp_value | ^~~~~~~ paramEst.cpp: In function ‘arma::vec estHasemanElston(const mat&, const mat&, const List&, const vec&)’: paramEst.cpp:302:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 302 | for (int i = 0; i < n; i++) { | ~~^~~ paramEst.cpp:303:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 303 | for (int j = i; j < n; j++) { | ~~^~~ paramEst.cpp:294:18: warning: unused variable ‘i’ [-Wunused-variable] 294 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:294:21: warning: unused variable ‘j’ [-Wunused-variable] 294 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:295:12: warning: unused variable ‘_ycovij’ [-Wunused-variable] 295 | double _ycovij; // Declare temp_value | ^~~~~~~ paramEst.cpp: In function ‘arma::vec estHasemanElstonConstrained(const mat&, const mat&, const List&, const vec&, arma::vec, const int&)’: paramEst.cpp:381:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 381 | for (int i = 0; i < n; i++) { | ~~^~~ paramEst.cpp:382:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 382 | for (int j = i; j < n; j++) { | ~~^~~ paramEst.cpp:373:18: warning: unused variable ‘i’ [-Wunused-variable] 373 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:373:21: warning: unused variable ‘j’ [-Wunused-variable] 373 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:374:12: warning: unused variable ‘_ycovij’ [-Wunused-variable] 374 | double _ycovij; // Declare temp_value | ^~~~~~~ paramEst.cpp: In function ‘arma::vec estHasemanElstonConstrainedGenetic(const mat&, const mat&, const List&, const vec&, const mat&, arma::vec, const int&)’: paramEst.cpp:490:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 490 | for (int i = 0; i < n; i++) { | ~~^~~ paramEst.cpp:491:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 491 | for (int j = i; j < n; j++) { | ~~^~~ paramEst.cpp:484:18: warning: unused variable ‘i’ [-Wunused-variable] 484 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:484:21: warning: unused variable ‘j’ [-Wunused-variable] 484 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:485:12: warning: unused variable ‘_ycovij’ [-Wunused-variable] 485 | double _ycovij; // Declare temp_value | ^~~~~~~ paramEst.cpp: In function ‘arma::vec nnlsSolve(const mat&, const vec&, arma::vec, const int&)’: paramEst.cpp:549:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 549 | for(int i=0; i < m; i++){ | ~~^~~ paramEst.cpp:559:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 559 | for(int i=0; i < m; i++){ | ~~^~~ paramEst.cpp:587:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 587 | for(int i=0; i < m; i++){ | ~~^~~ paramEst.cpp:623:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 623 | for(int i=0; i < m; i++){ | ~~^~~ paramEst.cpp:543:18: warning: variable ‘inner_count’ set but not used [-Wunused-but-set-variable] 543 | unsigned int inner_count = 0; | ^~~~~~~~~~~ paramEst.cpp:544:18: warning: unused variable ‘outer_count’ [-Wunused-variable] 544 | unsigned int outer_count = 0; | ^~~~~~~~~~~ paramEst.cpp: In function ‘arma::mat vectoriseZ(const mat&, const List&, const mat&)’: paramEst.cpp:688:9: warning: unused variable ‘j’ [-Wunused-variable] 688 | int j, k, l, a; | ^ paramEst.cpp:688:12: warning: unused variable ‘k’ [-Wunused-variable] 688 | int j, k, l, a; | ^ paramEst.cpp:688:15: warning: unused variable ‘l’ [-Wunused-variable] 688 | int j, k, l, a; | ^ paramEst.cpp:688:18: warning: unused variable ‘a’ [-Wunused-variable] 688 | int j, k, l, a; | ^ paramEst.cpp: In function ‘double phiLineSearch(double, double, double, const int&, const vec&, const mat&, double, const vec&, const vec&, const vec&)’: paramEst.cpp:866:12: warning: unused variable ‘half_logli’ [-Wunused-variable] 866 | double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood; | ^~~~~~~~~~ paramEst.cpp:871:10: warning: unused variable ‘comp_vals’ [-Wunused-variable] 871 | bool comp_vals = false; | ^~~~~~~~~ paramEst.cpp: In function ‘arma::mat vectoriseZ(const mat&, const List&, const mat&)’: paramEst.cpp:714:21: warning: ‘temp_value’ may be used uninitialized in this function [-Wmaybe-uninitialized] 714 | #pragma omp parallel for reduction(+:temp_value) | ^~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c pseudovarPartial.cpp -o pseudovarPartial.o pseudovarPartial.cpp: In function ‘Rcpp::List pseudovarPartial_P(Rcpp::List, const mat&)’: pseudovarPartial.cpp:58:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 58 | for (int j = 0; j < n; j++) { | ~~^~~ pseudovarPartial.cpp:61:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 61 | for (int k = 0; k < n; k++) { | ~~^~~ pseudovarPartial.cpp:64:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 64 | for(int a=0; a < n; a++){ | ~~^~~ pseudovarPartial.cpp:60:21: warning: ‘temp_value’ may be used uninitialized in this function [-Wmaybe-uninitialized] 60 | #pragma omp parallel for reduction(+:temp_value) | ^~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o miloR.so RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o utils.o -lopenblas -lgfortran -lm -fopenmp -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-miloR/00new/miloR/libs ** R ** data ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘graph’ in package ‘miloR’ ** help *** installing help indices ** 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 (miloR)