* installing *source* package ‘mapfit’ ... ** package ‘mapfit’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gamma.cpp -o gamma.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phase_dist.cpp -o phase_dist.o In file included from phase_dist.cpp:4: In file included from ./phase_gen.h:8: ./blas.h:95:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./blas.h:116:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./blas.h:138:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./blas.h:139:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ In file included from phase_dist.cpp:4: In file included from ./phase_gen.h:9: ./unif.h:12:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:18:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:45:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:85:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:77:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:126:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:117:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:118:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./unif.h:193:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:211:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./unif.h:236:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:262:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ In file included from phase_dist.cpp:4: ./phase_gen.h:232:10: warning: unused variable 'tllf' [-Wunused-variable] double tllf = 0.0; ^ ./phase_gen.h:230:10: warning: unused variable 'scale' [-Wunused-variable] double scale; ^ ./phase_gen.h:445:10: warning: unused variable 'tllf' [-Wunused-variable] double tllf = 0.0; ^ ./phase_gen.h:443:10: warning: unused variable 'scale' [-Wunused-variable] double scale; ^ 20 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c emfit_phase_gen.cpp -o emfit_phase_gen.o In file included from emfit_phase_gen.cpp:4: In file included from ./phase_gen.h:8: ./blas.h:95:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./blas.h:116:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./blas.h:138:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./blas.h:139:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ In file included from emfit_phase_gen.cpp:4: In file included from ./phase_gen.h:9: ./unif.h:12:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:18:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:45:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:85:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:77:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:126:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:117:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:118:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./unif.h:193:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:211:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./unif.h:236:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:262:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ In file included from emfit_phase_gen.cpp:4: ./phase_gen.h:232:10: warning: unused variable 'tllf' [-Wunused-variable] double tllf = 0.0; ^ ./phase_gen.h:230:10: warning: unused variable 'scale' [-Wunused-variable] double scale; ^ ./phase_gen.h:445:10: warning: unused variable 'tllf' [-Wunused-variable] double tllf = 0.0; ^ ./phase_gen.h:443:10: warning: unused variable 'scale' [-Wunused-variable] double scale; ^ 20 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c emfit_phase_cf1.cpp -o emfit_phase_cf1.o In file included from emfit_phase_cf1.cpp:4: In file included from ./phase_cf1.h:5: In file included from ./phase_gen.h:8: ./blas.h:95:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./blas.h:116:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./blas.h:138:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./blas.h:139:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ In file included from emfit_phase_cf1.cpp:4: In file included from ./phase_cf1.h:5: In file included from ./phase_gen.h:9: ./unif.h:12:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:18:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:45:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:85:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:77:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:126:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:117:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:118:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./unif.h:193:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:211:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./unif.h:236:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:262:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ In file included from emfit_phase_cf1.cpp:4: In file included from ./phase_cf1.h:5: ./phase_gen.h:232:10: warning: unused variable 'tllf' [-Wunused-variable] double tllf = 0.0; ^ ./phase_gen.h:230:10: warning: unused variable 'scale' [-Wunused-variable] double scale; ^ ./phase_gen.h:443:10: warning: unused variable 'scale' [-Wunused-variable] double scale; ^ ./phase_gen.h:445:10: warning: unused variable 'tllf' [-Wunused-variable] double tllf = 0.0; ^ 20 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c emfit_phase_herlang.cpp -o emfit_phase_herlang.o In file included from emfit_phase_herlang.cpp:4: In file included from ./phase_herlang.h:7: ./blas.h:95:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./blas.h:116:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./blas.h:139:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./blas.h:138:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ In file included from emfit_phase_herlang.cpp:4: ./phase_herlang.h:356:11: warning: unused variable 'alpha' [-Wunused-variable] double* alpha = trait2::value(model.alpha); ^ ./phase_herlang.h:378:11: warning: unused variable 'alpha' [-Wunused-variable] double* alpha = trait2::value(model.alpha); ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c emfit_map_gen.cpp -o emfit_map_gen.o In file included from emfit_map_gen.cpp:4: In file included from ./map_gen.h:8: ./blas.h:95:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./blas.h:116:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./blas.h:138:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./blas.h:139:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ In file included from emfit_map_gen.cpp:4: In file included from ./map_gen.h:10: ./unif.h:18:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:12:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:45:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:77:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:85:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:118:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./unif.h:117:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:126:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:193:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:211:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./unif.h:236:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:262:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ In file included from emfit_map_gen.cpp:4: ./map_gen.h:262:11: warning: unused variable 'alpha' [-Wunused-variable] double* alpha = stride_vector_traits<Mv>::value(model.alpha); ^ ./map_gen.h:256:17: warning: unused variable 'eb' [-Wunused-variable] const double* eb = stride_vector_traits<Ev>::value(eres.eb); ^ ./map_gen.h:320:11: warning: unused variable 'j' [-Wunused-variable] int j = colind1[z] - base1; ^ ./map_gen.h:304:11: warning: unused variable 'alpha' [-Wunused-variable] double* alpha = stride_vector_traits<Mv>::value(model.alpha); ^ ./map_gen.h:293:17: warning: unused variable 'eb' [-Wunused-variable] const double* eb = stride_vector_traits<Ev>::value(eres.eb); ^ ./map_gen.h:337:17: warning: unused variable 'eb' [-Wunused-variable] const double* eb = stride_vector_traits<Ev>::value(eres.eb); ^ ./map_gen.h:348:11: warning: unused variable 'alpha' [-Wunused-variable] double* alpha = stride_vector_traits<Mv>::value(model.alpha); ^ ./map_gen.h:411:9: warning: unused variable 'j' [-Wunused-variable] int j = colind1[z] - base1; ^ ./map_gen.h:381:17: warning: unused variable 'eb' [-Wunused-variable] const double* eb = stride_vector_traits<Ev>::value(eres.eb); ^ ./map_gen.h:394:11: warning: unused variable 'alpha' [-Wunused-variable] double* alpha = stride_vector_traits<Mv>::value(model.alpha); ^ 26 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c emfit_map_erhmm.cpp -o emfit_map_erhmm.o In file included from emfit_map_erhmm.cpp:4: In file included from ./map_erhmm.h:9: ./blas.h:95:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./blas.h:116:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./blas.h:139:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./blas.h:138:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ In file included from emfit_map_erhmm.cpp:4: ./map_erhmm.h:114:17: warning: unused variable 'eb' [-Wunused-variable] const double* eb = stride_vector_traits<Ev>::value(eres.eb); ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c emfit_map_gmmpp.cpp -o emfit_map_gmmpp.o In file included from emfit_map_gmmpp.cpp:4: In file included from ./map_gmmpp.h:7: ./blas.h:95:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./blas.h:116:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./blas.h:139:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./blas.h:138:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ In file included from emfit_map_gmmpp.cpp:4: In file included from ./map_gmmpp.h:8: ./unif.h:18:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:12:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:45:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:85:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:77:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:126:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0; ^ ./unif.h:118:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./unif.h:117:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:193:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:211:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./unif.h:236:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./unif.h:262:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ In file included from emfit_map_gmmpp.cpp:4: In file included from ./map_gmmpp.h:12: ./map_gen.h:256:17: warning: unused variable 'eb' [-Wunused-variable] const double* eb = stride_vector_traits<Ev>::value(eres.eb); ^ ./map_gen.h:262:11: warning: unused variable 'alpha' [-Wunused-variable] double* alpha = stride_vector_traits<Mv>::value(model.alpha); ^ ./map_gen.h:320:11: warning: unused variable 'j' [-Wunused-variable] int j = colind1[z] - base1; ^ ./map_gen.h:304:11: warning: unused variable 'alpha' [-Wunused-variable] double* alpha = stride_vector_traits<Mv>::value(model.alpha); ^ ./map_gen.h:293:17: warning: unused variable 'eb' [-Wunused-variable] const double* eb = stride_vector_traits<Ev>::value(eres.eb); ^ ./map_gen.h:337:17: warning: unused variable 'eb' [-Wunused-variable] const double* eb = stride_vector_traits<Ev>::value(eres.eb); ^ ./map_gen.h:348:11: warning: unused variable 'alpha' [-Wunused-variable] double* alpha = stride_vector_traits<Mv>::value(model.alpha); ^ ./map_gen.h:411:9: warning: unused variable 'j' [-Wunused-variable] int j = colind1[z] - base1; ^ ./map_gen.h:394:11: warning: unused variable 'alpha' [-Wunused-variable] double* alpha = stride_vector_traits<Mv>::value(model.alpha); ^ ./map_gen.h:381:17: warning: unused variable 'eb' [-Wunused-variable] const double* eb = stride_vector_traits<Ev>::value(eres.eb); ^ In file included from emfit_map_gmmpp.cpp:4: ./map_gmmpp.h:56:15: warning: variable 'dji' set but not used [-Wunused-but-set-variable] double dij, dji; ^ ./map_gmmpp.h:174:16: warning: unused variable 'tmax' [-Wunused-variable] const double tmax = data.maxtime; ^ emfit_map_gmmpp.cpp:63:8: warning: unused variable 'm' [-Wunused-variable] auto m = tdat.length(); ^ 29 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gth.cpp -o gth.o In file included from gth.cpp:4: In file included from ./gth.h:6: ./blas.h:95:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./blas.h:116:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ ./blas.h:139:13: warning: unused variable 'n' [-Wunused-variable] const int n = traits1::ncol(A); ^ ./blas.h:138:13: warning: unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A); ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o mapfit.so gamma.o phase_dist.o emfit_phase_gen.o emfit_phase_cf1.o emfit_phase_herlang.o emfit_map_gen.o emfit_map_erhmm.o emfit_map_gmmpp.o gth.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame installing to /Volumes/Builds/packages/big-sur-arm64/results/4.4/mapfit.Rcheck/00LOCK-mapfit/00new/mapfit/libs ** generating debug symbols (dSYM) ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** 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 (mapfit)