* 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)