* installing *source* package ‘mapfit’ ...
** this is package ‘mapfit’ version ‘1.0.1’
** package ‘mapfit’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/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/4.5/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phase_dist.cpp -o phase_dist.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c emfit_phase_gen.cpp -o emfit_phase_gen.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c emfit_phase_cf1.cpp -o emfit_phase_cf1.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c emfit_phase_herlang.cpp -o emfit_phase_herlang.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c emfit_map_gen.cpp -o emfit_map_gen.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/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_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]
In file included from emfit_map_gen.cpp const int n = traits1::ncol(A);:
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_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;In file included from
emfit_map_gen.cpp ^:4
:
In file included from ./map_gen.h:10:
./unif.h./unif.h::45:127::13 warning: :variable 'maxi' set but not used [-Wunused-but-set-variable]
int maxi = 0;warning:
unused variable 'm' [-Wunused-variable] ^
const int m = traits1::nrow(A);
^
./unif.h:./unif.h77:18::713:: warning: warning: unused variable 'm' [-Wunused-variable]variable 'maxi' set but not used [-Wunused-but-set-variable]
const int m = traits1::nrow(A);
int maxi = 0; ^
^./unif.h
:85:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable]
./unif.h int maxi = 0;:
45 ^:
7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable]
./unif.h int maxi = 0;:
117 ^:
13: warning: unused variable 'm' [-Wunused-variable]
const int m = traits1::nrow(A);
./unif.h ^:
77./unif.h::11813:13:: warning: warning: unused variable 'm' [-Wunused-variable]unused variable 'n' [-Wunused-variable]
const int m = traits1::nrow(A); const int n = traits1::ncol(A);
^ ^
./unif.h./unif.h::85126::77:: warning: variable 'maxi' set but not used [-Wunused-but-set-variable]warning:
variable 'maxi' set but not used [-Wunused-but-set-variable] int maxi = 0;
int maxi = 0; ^
^
./unif.h:117./unif.h::19313:13:: warning: warning: unused variable 'm' [-Wunused-variable]unused variable 'm' [-Wunused-variable]
const int m = traits1::nrow(A); const int m = traits1::nrow(A);
^ ^
./unif.h./unif.h:118:211::1313:: warning: warning: unused variable 'n' [-Wunused-variable]unused variable 'n' [-Wunused-variable]
const int n = traits1::ncol(A); const int n = traits1::ncol(A);
^
^./unif.h
:126:7./unif.h: :236warning: :variable 'maxi' set but not used [-Wunused-but-set-variable]
13 int maxi = 0;:
^
warning: unused variable 'm' [-Wunused-variable]
const int m = traits1::nrow(A);In file included from emfit_phase_herlang.cpp
: ^./unif.h4::
In file included from 193./phase_herlang.h::713./unif.h:
::./blas.h262: :9513warning: ::unused variable 'm' [-Wunused-variable] 13
warning: : const int m = traits1::nrow(A); unused variable 'm' [-Wunused-variable]
^
warning: const int m = traits1::nrow(A);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:8:
./blas.h:95:./unif.h./blas.h:13:211:116: :warning: 1313unused variable 'n' [-Wunused-variable]:
: const int n = traits1::ncol(A);warning: warning:
unused variable 'n' [-Wunused-variable] ^unused variable 'm' [-Wunused-variable]
const int n = traits1::ncol(A);
const int m = traits1::nrow(A); ^
^
./blas.h./unif.h::116236::1313:: ./blas.hwarning: warning: unused variable 'm' [-Wunused-variable]unused variable 'm' [-Wunused-variable]:
138 const int m = traits1::nrow(A); const int m = traits1::nrow(A);:13
^ ^:
warning: ./unif.hunused variable 'm' [-Wunused-variable]:
262 const int m = traits1::nrow(A);:13
:./blas.h ^warning: :
unused variable 'm' [-Wunused-variable]138./blas.h:
13:139 const int m = traits1::nrow(A);::
warning: 13unused variable 'm' [-Wunused-variable]:
^ const int m = traits1::nrow(A);
warning:
unused variable 'n' [-Wunused-variable] ^
const int n = traits1::ncol(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:
./phase_gen.h:230:10: warning: unused variable 'scale' [-Wunused-variable]
double scale;
^
./phase_gen.h:232:10: warning: unused variable 'tllf' [-Wunused-variable]
double tllf = 0.0;
^
./phase_gen.h:443:10: warning: unused variable 'scale' [-Wunused-variable]
double scale;
^
./phase_gen.h:445:10:In file included from In file included from phase_dist.cppwarning: :emfit_phase_cf1.cpp4:
unused variable 'tllf' [-Wunused-variable]:In file included from
./phase_gen.h4 double tllf = 0.0;:
^:
9In file included from :
./phase_cf1.h./unif.h::512::
13:In file included from ./phase_gen.hwarning: :unused variable 'm' [-Wunused-variable]
8:
const int m = traits1::nrow(A);./blas.h
: ^95:
13:./unif.h :18warning: :In file included from 7:emfit_map_gen.cppunused variable 'n' [-Wunused-variable]:
const int n = traits1::ncol(A); 4
warning: ^variable 'maxi' set but not used [-Wunused-but-set-variable]:
./map_gen.h int maxi = 0;:
256 ^:
17: warning: unused variable 'eb' [-Wunused-variable]
const double* eb = stride_vector_traits<Ev>::value(eres.eb);
^
./blas.h./map_gen.h::262116::./unif.h:114513::: warning: 7unused variable 'alpha' [-Wunused-variable]warning:
unused variable 'm' [-Wunused-variable]:
double* alpha = stride_vector_traits<Mv>::value(model.alpha); const int m = traits1::nrow(A);
warning: ^ ^variable 'maxi' set but not used [-Wunused-but-set-variable]
int maxi = 0;
^
./blas.h:./unif.h138::7713::13 :warning: unused variable 'm' [-Wunused-variable]warning:
unused variable 'm' [-Wunused-variable] const int m = traits1::nrow(A);
const int m = traits1::nrow(A);
./map_gen.h ^ ^
:
./blas.h320::./unif.h139:11:85:13 ::warning: 7unused variable 'j' [-Wunused-variable]warning: unused variable 'n' [-Wunused-variable]:
int j = colind1[z] - base1; const int n = traits1::ncol(A);warning:
variable 'maxi' set but not used [-Wunused-but-set-variable]
^ int maxi = 0;
^ ^
./map_gen.h:293:17: ./unif.hwarning: :unused variable 'eb' [-Wunused-variable]117
:13 const double* eb = stride_vector_traits<Ev>::value(eres.eb);
: ^ warning:
./map_gen.hunused variable 'm' [-Wunused-variable]:
const int m = traits1::nrow(A);304
: ^11:
./unif.hwarning: :unused variable 'alpha' [-Wunused-variable]
118 double* alpha = stride_vector_traits<Mv>::value(model.alpha);:In file included from 13
:emfit_phase_herlang.cpp ^ :
warning: 4:
./phase_herlang.hunused variable 'n' [-Wunused-variable]:
356 const int n = traits1::ncol(A);:11
: ^warning:
unused variable 'alpha' [-Wunused-variable]./map_gen.h
./unif.h double* alpha = trait2::value(model.alpha);:
: ^337
126::177:: warning: warning: unused variable 'eb' [-Wunused-variable]variable 'maxi' set but not used [-Wunused-but-set-variable]
int maxi = 0; const double* eb = stride_vector_traits<Ev>::value(eres.eb);
./phase_herlang.h ^
:
378 ^:
11./map_gen.h:: warning: unused variable 'alpha' [-Wunused-variable]348
./unif.h double* alpha = trait2::value(model.alpha);::11
193: ^:
warning: 13unused variable 'alpha' [-Wunused-variable]
: double* alpha = stride_vector_traits<Mv>::value(model.alpha); warning:
^unused variable 'm' [-Wunused-variable]
const int m = traits1::nrow(A);
^
./unif.h:211:./map_gen.h13::411 :warning: 9unused variable 'n' [-Wunused-variable]:
warning: const int n = traits1::ncol(A);
unused variable 'j' [-Wunused-variable] ^
./unif.h int j = colind1[z] - base1;:
236 ^
:13:./map_gen.h :warning: 381unused variable 'm' [-Wunused-variable]:
17: const int m = traits1::nrow(A); warning:
unused variable 'eb' [-Wunused-variable]
^ const double* eb = stride_vector_traits<Ev>::value(eres.eb);
^
./map_gen.h:394:11:./unif.h :warning: unused variable 'alpha' [-Wunused-variable]262
: double* alpha = stride_vector_traits<Mv>::value(model.alpha);13
: ^
In file included from warning: emfit_phase_cf1.cpp:unused variable 'm' [-Wunused-variable]4
:
const int m = traits1::nrow(A);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: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: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: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: In file included from unused variable 'm' [-Wunused-variable]phase_dist.cpp
: const int m = traits1::nrow(A);4
^:
./phase_gen.h:230:10: warning: unused variable 'scale' [-Wunused-variable]
double scale;
^
./phase_gen.h:232:10: warning: unused variable 'tllf' [-Wunused-variable]
double tllf = 0.0;
^
./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;
^
In file included from emfit_phase_cf1.cpp:4:
In file included from ./phase_cf1.h:5:
./phase_gen.h:230:10: warning: unused variable 'scale' [-Wunused-variable]
double scale;
^
./phase_gen.h:232:10: warning: unused variable 'tllf' [-Wunused-variable]
double tllf = 0.0;
^
./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;
^
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: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_erhmm.cpp:4:
./map_erhmm.h:114:17: warning: unused variable 'eb' [-Wunused-variable]
const double* eb = stride_vector_traits<Ev>::value(eres.eb);
^
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/4.5/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c emfit_map_gmmpp.cpp -o emfit_map_gmmpp.o
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/4.5/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gth.cpp -o gth.o
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/4.5/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
26 warnings generated.
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: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_gmmpp.cpp:4:
In file included from ./map_gmmpp.h:8:
./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: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: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: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_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:293:17: warning: unused variable 'eb' [-Wunused-variable]
const double* eb = stride_vector_traits<Ev>::value(eres.eb);
^
./map_gen.h:304:11: warning: unused variable 'alpha' [-Wunused-variable]
double* alpha = stride_vector_traits<Mv>::value(model.alpha);
^
./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);
^
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();
^
20 warnings generated.
20 warnings generated.
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: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);
^
4 warnings generated.
29 warnings generated.
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-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
ld: warning: could not create compact unwind for _allocate_tramp_ctrl: does not use standard frame
ld: warning: could not create compact unwind for ___gcc_nested_func_ptr_created: does not use standard frame
ld: warning: could not create compact unwind for ___gcc_nested_func_ptr_deleted: does not use standard frame
ld: warning: could not create compact unwind for ___emutls_get_address: does not use standard frame
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.5/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)