install for i386
* installing *source* package 'GRENITS' ...
** libs
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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]
AR1_Gauss_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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]
AR1_Student_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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]
AR1_biocond.cc:48:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c R_C_interface.cpp -o R_C_interface.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c commonFunctions.cc -o commonFunctions.o
commonFunctions.cc:22:66: warning: declaration of 'void dtrtrs_(char*, char*, char*, arma::blas_int*, arma::blas_int*, double*, arma::blas_int*, double*, arma::blas_int*, arma::blas_int*)' with C language linkage [enabled by default]
E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include/armadillo_bits/lapack_bones.hpp:324:1: warning: conflicts with previous declaration 'void arma::dtrtrs_(char*, char*, char*, arma::blas_int*, arma::blas_int*, const double*, arma::blas_int*, double*, arma::blas_int*, arma::blas_int*)' [enabled by default]
commonFunctions.cc: In function 'void random_intSequence(arma::ucolvec&)':
commonFunctions.cc:270:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
commonFunctions.cc: In function 'void estimateRemainingTime(double&, double&, int, int, clock_t&)':
commonFunctions.cc:317:36: warning: variable 'so_far_clock' set but not used [-Wunused-but-set-variable]
commonFunctions.cc: In function 'void processFixedGammas(arma::mat&, int&, int&, arma::umat&, arma::umat&, arma::ucolvec&, arma::umat&, arma::uvec&, arma::uvec&)':
commonFunctions.cc:377:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
commonFunctions.cc:380:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
commonFunctions.cc: In function 'void updateCoefficients_reg(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&, const ucolvec&)':
commonFunctions.cc:440:59: warning: unused variable 'num_on' [-Wunused-variable]
commonFunctions.cc: In function 'void updateCoefficients(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&)':
commonFunctions.cc:482:59: warning: unused variable 'num_on' [-Wunused-variable]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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:128:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
updateFunctions_AR1.cc:134:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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:186:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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]
updateFunctions_Splines.cc:158:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable]
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]
updateFunctions_Splines.cc:182:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable]
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:296:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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:478:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
updateFunctions_Splines.cc: In function 'void fixedBasesFromFixedRegs(arma::umat&, arma::umat&, arma::ucolvec&, int)':
updateFunctions_Splines.cc:714:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -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 E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/lib/i386/libRcpp.a -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lRlapack -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/GRENITS.buildbin-libdir/GRENITS/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'GRENITS_package.Rnw'
** testing if installed package can be loaded
install for x64
* installing *source* package 'GRENITS' ...
** libs
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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]
AR1_Gauss_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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]
AR1_Student_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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]
AR1_biocond.cc:48:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c R_C_interface.cpp -o R_C_interface.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c commonFunctions.cc -o commonFunctions.o
commonFunctions.cc:22:66: warning: declaration of 'void dtrtrs_(char*, char*, char*, arma::blas_int*, arma::blas_int*, double*, arma::blas_int*, double*, arma::blas_int*, arma::blas_int*)' with C language linkage [enabled by default]
E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include/armadillo_bits/lapack_bones.hpp:324:1: warning: conflicts with previous declaration 'void arma::dtrtrs_(char*, char*, char*, arma::blas_int*, arma::blas_int*, const double*, arma::blas_int*, double*, arma::blas_int*, arma::blas_int*)' [enabled by default]
commonFunctions.cc: In function 'void random_intSequence(arma::ucolvec&)':
commonFunctions.cc:270:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
commonFunctions.cc: In function 'void estimateRemainingTime(double&, double&, int, int, clock_t&)':
commonFunctions.cc:317:36: warning: variable 'so_far_clock' set but not used [-Wunused-but-set-variable]
commonFunctions.cc: In function 'void processFixedGammas(arma::mat&, int&, int&, arma::umat&, arma::umat&, arma::ucolvec&, arma::umat&, arma::uvec&, arma::uvec&)':
commonFunctions.cc:377:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
commonFunctions.cc:380:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
commonFunctions.cc: In function 'void updateCoefficients_reg(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&, const ucolvec&)':
commonFunctions.cc:440:59: warning: unused variable 'num_on' [-Wunused-variable]
commonFunctions.cc: In function 'void updateCoefficients(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&)':
commonFunctions.cc:482:59: warning: unused variable 'num_on' [-Wunused-variable]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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:128:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
updateFunctions_AR1.cc:134:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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:186:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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]
updateFunctions_Splines.cc:158:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable]
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]
updateFunctions_Splines.cc:182:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable]
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:296:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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:478:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
updateFunctions_Splines.cc: In function 'void fixedBasesFromFixedRegs(arma::umat&, arma::umat&, arma::ucolvec&, int)':
updateFunctions_Splines.cc:714:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -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 E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/lib/x64/libRcpp.a -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lRlapack -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/GRENITS.buildbin-libdir/GRENITS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GRENITS' as GRENITS_1.11.0.zip
* DONE (GRENITS)