############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GRENITS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘GRENITS’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o AR1_Gauss_biocond.cc: In function ‘void Error_Gauss_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)’: AR1_Gauss_biocond.cc:49:30: warning: unused variable ‘numDiag’ [-Wunused-variable] 49 | int num_fixedON, numDiag, p_sqr, free_gammas; | ^~~~~~~ AR1_Gauss_biocond.cc:49:39: warning: variable ‘p_sqr’ set but not used [-Wunused-but-set-variable] 49 | int num_fixedON, numDiag, p_sqr, free_gammas; | ^~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c AR1_Student_biocond.cc -o AR1_Student_biocond.o AR1_Student_biocond.cc: In function ‘void Error_Student_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)’: AR1_Student_biocond.cc:49:30: warning: unused variable ‘numDiag’ [-Wunused-variable] 49 | int num_fixedON, numDiag, p_sqr, free_gammas; | ^~~~~~~ AR1_Student_biocond.cc:49:39: warning: variable ‘p_sqr’ set but not used [-Wunused-but-set-variable] 49 | int num_fixedON, numDiag, p_sqr, free_gammas; | ^~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c AR1_biocond.cc -o AR1_biocond.o AR1_biocond.cc: In function ‘void AR1_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)’: AR1_biocond.cc:48:30: warning: unused variable ‘numDiag’ [-Wunused-variable] 48 | int num_fixedON, numDiag, p_sqr, free_gammas; | ^~~~~~~ AR1_biocond.cc:48:39: warning: variable ‘p_sqr’ set but not used [-Wunused-but-set-variable] 48 | int num_fixedON, numDiag, p_sqr, free_gammas; | ^~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c PSplines_biocond.cc -o PSplines_biocond.o PSplines_biocond.cc: In function ‘void PSplines_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)’: PSplines_biocond.cc:45:63: warning: unused variable ‘numDiag’ [-Wunused-variable] 45 | int num_fixedON, nodesSpline, degreeSpline, numDiag, free_gammas; | ^~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c R_C_interface.cpp -o R_C_interface.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c commonFunctions.cc -o commonFunctions.o commonFunctions.cc: In function ‘void random_intSequence(arma::ucolvec&)’: commonFunctions.cc:268:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 268 | for (int i = 0; i < seq.n_elem; i++) | ~~^~~~~~~~~~~~ commonFunctions.cc: In function ‘void estimateRemainingTime(double&, double&, int, int, clock_t&)’: commonFunctions.cc:315:36: warning: variable ‘so_far_clock’ set but not used [-Wunused-but-set-variable] 315 | clock_t so_far_clock, time_now; //so_far_sec, | ^~~~~~~~~~~~ commonFunctions.cc: In function ‘void processFixedGammas(arma::mat&, int&, int&, arma::umat&, arma::umat&, arma::ucolvec&, arma::umat&, arma::uvec&, arma::uvec&)’: commonFunctions.cc:375:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 375 | for(int i = 0; i!=Gamma_fixed.n_cols;i++) | ~^~~~~~~~~~~~~~~~~~~~ commonFunctions.cc:378:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 378 | for(int j = 0; j!=Gamma_fixed.n_cols;j++) | ~^~~~~~~~~~~~~~~~~~~~ commonFunctions.cc: In function ‘void updateCoefficients_reg(arma::mat&, const int&, const arma::urowvec&, const arma::mat&, const arma::rowvec&, const arma::ucolvec&)’: commonFunctions.cc:438:59: warning: unused variable ‘num_on’ [-Wunused-variable] 438 | unsigned int num_on; | ^~~~~~ commonFunctions.cc: In function ‘void updateCoefficients(arma::mat&, const int&, const arma::urowvec&, const arma::mat&, const arma::rowvec&)’: commonFunctions.cc:480:59: warning: unused variable ‘num_on’ [-Wunused-variable] 480 | unsigned int num_on; | ^~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c functionsErrorModel.cc -o functionsErrorModel.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c updateFunctions_AR1.cc -o updateFunctions_AR1.o updateFunctions_AR1.cc: In function ‘void updateCoeffAndGibbsVars(arma::mat&, arma::umat&, const arma::colvec&, const arma::mat&, const arma::mat&, const arma::mat&, const double&, const unsigned int&)’: updateFunctions_AR1.cc:128:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 128 | for(int j_loop = 0; j_loop < genes; j_loop++) | ~~~~~~~^~~~~~~ updateFunctions_AR1.cc:134:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 134 | if (i != j) | ~~^~~~ updateFunctions_AR1.cc: In function ‘void updateCoeffAndGibbsVars_reg(arma::mat&, arma::umat&, const arma::colvec&, const arma::mat&, const arma::mat&, double, const double&, const unsigned int&, arma::umat&, arma::ucolvec&, arma::umat&)’: updateFunctions_AR1.cc:186:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 186 | for(int j_loop = 0; j_loop < seq_rnd.n_elem; j_loop++) | ~~~~~~~^~~~~~~~~~~~~~~~ updateFunctions_AR1.cc: In function ‘void calc_logMVPDF_withLinks(double&, const arma::mat&, const arma::rowvec&, arma::urowvec&)’: updateFunctions_AR1.cc:264:59: warning: unused variable ‘num_on’ [-Wunused-variable] 264 | unsigned int num_on; | ^~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c updateFunctions_Splines.cc -o updateFunctions_Splines.o updateFunctions_Splines.cc: In function ‘void initBasesOn_rowvec(arma::urowvec&, const arma::urowvec&, int, int)’: updateFunctions_Splines.cc:158:16: warning: variable ‘start_indx’ set but not used [-Wunused-but-set-variable] 158 | int G, start_indx, end_indx; | ^~~~~~~~~~ updateFunctions_Splines.cc:158:28: warning: variable ‘end_indx’ set but not used [-Wunused-but-set-variable] 158 | int G, start_indx, end_indx; | ^~~~~~~~ updateFunctions_Splines.cc: In function ‘void initBasesOn(arma::urowvec&, const arma::umat&, int, int)’: updateFunctions_Splines.cc:182:16: warning: variable ‘start_indx’ set but not used [-Wunused-but-set-variable] 182 | int G, start_indx, end_indx; | ^~~~~~~~~~ updateFunctions_Splines.cc:182:28: warning: variable ‘end_indx’ set but not used [-Wunused-but-set-variable] 182 | int G, start_indx, end_indx; | ^~~~~~~~ updateFunctions_Splines.cc: In function ‘void updateTaus_reg(arma::mat&, arma::colvec&, const arma::mat&, arma::urowvec&, const arma::mat&, double, double, int, double, double, double, double, int, double, arma::uvec)’: updateFunctions_Splines.cc:296:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 296 | if(i == indxReg) | ~~^~~~~~~~~~ updateFunctions_Splines.cc: In function ‘void updateGammaAndB_row_i_reg(arma::mat&, arma::umat&, const arma::mat&, const arma::rowvec&, const arma::colvec&, int, int, int, arma::urowvec&, const arma::ucolvec&, const arma::urowvec&, const arma::ucolvec&, const arma::uvec&)’: updateFunctions_Splines.cc:478:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 478 | for(int j_loop = 0; j_loop < seq_rnd.n_elem; j_loop++) | ~~~~~~~^~~~~~~~~~~~~~~~ updateFunctions_Splines.cc: In function ‘void fixedBasesFromFixedRegs(arma::umat&, arma::umat&, arma::ucolvec&, int)’: updateFunctions_Splines.cc:714:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 714 | for(base_k = 0; base_k != M; base_k++) | ~~~~~~~^~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o GRENITS.so AR1_Gauss_biocond.o AR1_Student_biocond.o AR1_biocond.o PSplines_biocond.o R_C_interface.o ReadMCMCFiles.o commonFunctions.o functionsErrorModel.o matrixManipulationFunctions.o updateFunctions_AR1.o updateFunctions_Splines.o -llapack -L/home/biocbuild/bbs-3.21-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-GRENITS/00new/GRENITS/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** 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 (GRENITS)