############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf GRENITS.buildbin-libdir && mkdir GRENITS.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=GRENITS.buildbin-libdir GRENITS_1.47.0.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'GRENITS' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o AR1_Gauss_biocond.cc: In function 'void Error_Gauss_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)': AR1_Gauss_biocond.cc:49:30: warning: unused variable 'numDiag' [-Wunused-variable] 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] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c AR1_Student_biocond.cc -o AR1_Student_biocond.o AR1_Student_biocond.cc: In function 'void Error_Student_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)': AR1_Student_biocond.cc:49:30: warning: unused variable 'numDiag' [-Wunused-variable] 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] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c AR1_biocond.cc -o AR1_biocond.o AR1_biocond.cc: In function 'void AR1_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)': AR1_biocond.cc:48:30: warning: unused variable 'numDiag' [-Wunused-variable] 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] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c PSplines_biocond.cc -o PSplines_biocond.o PSplines_biocond.cc: In function 'void PSplines_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)': PSplines_biocond.cc:45:63: warning: unused variable 'numDiag' [-Wunused-variable] int num_fixedON, nodesSpline, degreeSpline, numDiag, free_gammas; ^~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_C_interface.cpp -o R_C_interface.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 uword' {aka 'const unsigned int'} [-Wsign-compare] 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] 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 uword' {aka 'const unsigned int'} [-Wsign-compare] 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 uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j = 0; j!=Gamma_fixed.n_cols;j++) ~^~~~~~~~~~~~~~~~~~~~ commonFunctions.cc: In function 'void updateCoefficients_reg(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&, const ucolvec&)': commonFunctions.cc:438:59: warning: unused variable 'num_on' [-Wunused-variable] unsigned int num_on; ^~~~~~ commonFunctions.cc: In function 'void updateCoefficients(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&)': commonFunctions.cc:480:59: warning: unused variable 'num_on' [-Wunused-variable] unsigned int num_on; ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c functionsErrorModel.cc -o functionsErrorModel.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c updateFunctions_AR1.cc -o updateFunctions_AR1.o updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars(arma::mat&, arma::umat&, const colvec&, const mat&, const mat&, const 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] for(int j_loop = 0; j_loop < genes; j_loop++) ~~~~~~~^~~~~~~ updateFunctions_AR1.cc:134:8: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if (i != j) ~~^~~~ updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars_reg(arma::mat&, arma::umat&, const colvec&, const mat&, const 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 uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j_loop = 0; j_loop < seq_rnd.n_elem; j_loop++) ~~~~~~~^~~~~~~~~~~~~~~~ updateFunctions_AR1.cc: In function 'void calc_logMVPDF_withLinks(double&, const mat&, const rowvec&, arma::urowvec&)': updateFunctions_AR1.cc:264:59: warning: unused variable 'num_on' [-Wunused-variable] unsigned int num_on; ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c updateFunctions_Splines.cc -o updateFunctions_Splines.o updateFunctions_Splines.cc: In function 'void initBasesOn_rowvec(arma::urowvec&, const urowvec&, int, int)': updateFunctions_Splines.cc:158:16: warning: variable 'start_indx' set but not used [-Wunused-but-set-variable] int G, start_indx, end_indx; ^~~~~~~~~~ updateFunctions_Splines.cc:158:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable] int G, start_indx, end_indx; ^~~~~~~~ updateFunctions_Splines.cc: In function 'void initBasesOn(arma::urowvec&, const umat&, int, int)': updateFunctions_Splines.cc:182:16: warning: variable 'start_indx' set but not used [-Wunused-but-set-variable] int G, start_indx, end_indx; ^~~~~~~~~~ updateFunctions_Splines.cc:182:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable] int G, start_indx, end_indx; ^~~~~~~~ updateFunctions_Splines.cc: In function 'void updateTaus_reg(arma::mat&, arma::colvec&, const mat&, arma::urowvec&, const 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] if(i == indxReg) ~~^~~~~~~~~~ updateFunctions_Splines.cc: In function 'void updateGammaAndB_row_i_reg(arma::mat&, arma::umat&, const mat&, const rowvec&, const colvec&, int, int, int, arma::urowvec&, const ucolvec&, const urowvec&, const ucolvec&, const uvec&)': updateFunctions_Splines.cc:478:30: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] 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] for(base_k = 0; base_k != M; base_k++) ~~~~~~~^~~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o GRENITS.dll tmp.def 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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/meat/GRENITS.buildbin-libdir/00LOCK-GRENITS/00new/GRENITS/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GRENITS' finding HTML links ... done LockeData html LockeDataError html analyse.output html defaultParams_gauss html defaultParams_linear html defaultParams_nonLinear html defaultParams_student html function_LinearNet html function_NonLinearNet html function_ReplicatesNet_gauss html function_ReplicatesNet_student html plotPriors html readChains html ** 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 * MD5 sums packaged installation of 'GRENITS' as GRENITS_1.47.0.zip * DONE (GRENITS)