* installing *source* package ‘mapfit’ ...
** package ‘mapfit’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/mapfit/src'
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c gamma.cpp -o gamma.o
In file included from gamma.cpp:2:
gamma.h:11:15: warning: 'gam::LOG_PI' defined but not used [-Wunused-variable]
11 | static double LOG_PI = 1.14472988584940017; // log(pi)
| ^~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c phase_dist.cpp -o phase_dist.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c emfit_phase_gen.cpp -o emfit_phase_gen.o
In file included from phase_gen.h:9,
from phase_dist.cpp:4:
unif.h: In instantiation of 'double _unif_::unif(T1&, double, CSCMatrixT) [with T1 = S4matrix<CSCMatrixT>]':
unif.h:154:22: required from 'double unif(T1&, double) [with T1 = S4matrix<CSCMatrixT>]'
154 | return _unif_::unif(A, ufactor, typename matrix_category<T1>::type{});
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase_dist.cpp:28:19: required from here
28 | double qv = unif(P, ufactor);
| ~~~~^~~~~~~~~~~~
unif.h:77:13: warning: unused variable 'm' [-Wunused-variable]
77 | const int m = traits1::nrow(A);
| ^
unif.h:85:7: warning: variable 'maxi' set but not used [-Wunused-but-set-variable]
85 | int maxi = 0;
| ^~~~
In file included from phase_gen.h:7:
gamma.h:24:15: warning: 'gam::B16' defined but not used [-Wunused-variable]
24 | static double B16 = (-3617.0 / 510.0);
| ^~~
gamma.h:23:15: warning: 'gam::B14' defined but not used [-Wunused-variable]
23 | static double B14 = ( 7.0 / 6.0);
| ^~~
gamma.h:22:15: warning: 'gam::B12' defined but not used [-Wunused-variable]
22 | static double B12 = (-691.0 / 2730.0);
| ^~~
gamma.h:21:15: warning: 'gam::B10' defined but not used [-Wunused-variable]
21 | static double B10 = ( 5.0 / 66.0);
| ^~~
gamma.h:20:15: warning: 'gam::B8' defined but not used [-Wunused-variable]
20 | static double B8 = (-1.0 / 30.0);
| ^~
gamma.h:19:15: warning: 'gam::B6' defined but not used [-Wunused-variable]
19 | static double B6 = ( 1.0 / 42.0);
| ^~
gamma.h:18:15: warning: 'gam::B4' defined but not used [-Wunused-variable]
18 | static double B4 = (-1.0 / 30.0);
| ^~
gamma.h:17:15: warning: 'gam::B2' defined but not used [-Wunused-variable]
17 | static double B2 = ( 1.0 / 6.0);
| ^~
gamma.h:14:12: warning: 'gam::N' defined but not used [-Wunused-variable]
14 | static int N = 8;
| ^
gamma.h:11:15: warning: 'gam::LOG_PI' defined but not used [-Wunused-variable]
11 | static double LOG_PI = 1.14472988584940017; // log(pi)
| ^~~~~~
gamma.h:10:15: warning: 'gam::LOG_2PI' defined but not used [-Wunused-variable]
10 | static double LOG_2PI = 1.83787706640934548;
| ^~~~~~~
gamma.h:9:15: warning: 'gam::PI' defined but not used [-Wunused-variable]
9 | static double PI = 3.14159265358979324; // pi
| ^~
In file included from phase_gen.h:9,
from emfit_phase_gen.cpp:4:
unif.h: In instantiation of 'void _diag_::diag(const T1&, T2&, CSCMatrixT) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Vector<13>]':
unif.h:287:15: required from 'void diag(const T1&, T2&) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Vector<13>]'
287 | _diag_::diag(A, diag_index, typename matrix_category<T1>::type{});
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit_phase_gen.cpp:30:7: required from here
30 | diag(Q, di);
| ~~~~^~~~~~~
unif.h:236:13: warning: unused variable 'm' [-Wunused-variable]
236 | const int m = traits1::nrow(A);
| ^
phase_gen.h: In instantiation of 'double estep(const GPH<T1, T2, T0>&, const PHGroupSample<T4, T5, T6>&, GPHEres<T7, T8>&, OptionT&, WorkSpace&) [with T0 = Rcpp::Vector<13>; T1 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T2 = S4matrix<CSCMatrixT>; T4 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T5 = Rcpp::Vector<13>; T6 = Rcpp::Vector<13>; T7 = std::vector<double>; T8 = S4matrix<CSCMatrixT>; OptionT = EMOptions; WorkSpace = GPHWorkSpace2]':
emfit.h:56:19: required from 'void emfit(ModelT&, const DataT&, OptionT&, ET&, WorkSpace&) [with ModelT = GPH<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<CSCMatrixT>, Rcpp::Vector<13> >; DataT = PHGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; OptionT = EMOptions; ET = GPHEres<std::vector<double>, S4matrix<CSCMatrixT> >; WorkSpace = GPHWorkSpace2]'
56 | prev_llf = estep(model, data, eres, options, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit_phase_gen.cpp:122:8: required from here
122 | emfit(model, dat, opts, eres, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase_gen.h:230:10: warning: unused variable 'scale' [-Wunused-variable]
230 | double scale;
| ^~~~~
phase_gen.h:232:10: warning: unused variable 'tllf' [-Wunused-variable]
232 | double tllf = 0.0;
| ^~~~
phase_gen.h: In instantiation of 'double estep(const GPHPoi<GPH<T1, T2, T0> >&, const PHGroupSample<T4, T5, T6>&, GPHEres<T7, T8>&, OptionT&, WorkSpace&) [with T0 = Rcpp::Vector<13>; T1 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T2 = S4matrix<CSCMatrixT>; T4 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T5 = Rcpp::Vector<13>; T6 = Rcpp::Vector<13>; T7 = std::vector<double>; T8 = S4matrix<CSCMatrixT>; OptionT = EMOptions; WorkSpace = GPHWorkSpace2]':
emfit.h:56:19: required from 'void emfit(ModelT&, const DataT&, OptionT&, ET&, WorkSpace&) [with ModelT = GPHPoi<GPH<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<CSCMatrixT>, Rcpp::Vector<13> > >; DataT = PHGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; OptionT = EMOptions; ET = GPHEres<std::vector<double>, S4matrix<CSCMatrixT> >; WorkSpace = GPHWorkSpace2]'
56 | prev_llf = estep(model, data, eres, options, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit_phase_gen.cpp:189:8: required from here
189 | emfit(model, dat, opts, eres, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase_gen.h:443:10: warning: unused variable 'scale' [-Wunused-variable]
443 | double scale;
| ^~~~~
phase_gen.h:445:10: warning: unused variable 'tllf' [-Wunused-variable]
445 | double tllf = 0.0;
| ^~~~
In file included from phase_gen.h:8:
blas.h: In instantiation of 'void _mcopy_::mcopy(const T1&, T2&, CSCMatrixT, DenseMatrixT) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Matrix<14>]':
blas.h:165:17: required from 'void mcopy(const T1&, T2&) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Matrix<14>]'
165 | _mcopy_::mcopy(
| ~~~~~~~~~~~~~~^
166 | A, B,
| ~~~~~
167 | typename matrix_category<T1>::type{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
168 | typename matrix_category<T2>::type{});
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blas.h:1374:8: required from 'int _gesv_::gesv(TRANS, double, const T1&, const T2&, T3&, CSCMatrixT) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T3 = std::vector<double>]'
1374 | mcopy(A, tmpA);
| ~~~~~^~~~~~~~~
blas.h:1403:22: required from 'int gesv(const T0&, double, const T1&, const T2&, T3&) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T3 = std::vector<double>; T0 = TRANS]'
1403 | return _gesv_::gesv(tr, alpha, A, B, C,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
1404 | typename matrix_category<T1>::type{});
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase_gen.h:209:7: required from 'double estep(const GPH<T1, T2, T0>&, const PHGroupSample<T4, T5, T6>&, GPHEres<T7, T8>&, OptionT&, WorkSpace&) [with T0 = Rcpp::Vector<13>; T1 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T2 = S4matrix<CSCMatrixT>; T4 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T5 = Rcpp::Vector<13>; T6 = Rcpp::Vector<13>; T7 = std::vector<double>; T8 = S4matrix<CSCMatrixT>; OptionT = EMOptions; WorkSpace = GPHWorkSpace2]'
209 | gesv(TRANS{}, -1.0, model.Q, model.alpha, baralpha);
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit.h:56:19: required from 'void emfit(ModelT&, const DataT&, OptionT&, ET&, WorkSpace&) [with ModelT = GPH<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<CSCMatrixT>, Rcpp::Vector<13> >; DataT = PHGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; OptionT = EMOptions; ET = GPHEres<std::vector<double>, S4matrix<CSCMatrixT> >; WorkSpace = GPHWorkSpace2]'
56 | prev_llf = estep(model, data, eres, options, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit_phase_gen.cpp:122:8: required from here
122 | emfit(model, dat, opts, eres, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blas.h:116:13: warning: unused variable 'm' [-Wunused-variable]
116 | const int m = traits1::nrow(A);
| ^
In file included from phase_gen.h:7:
gamma.h:24:15: warning: 'gam::B16' defined but not used [-Wunused-variable]
24 | static double B16 = (-3617.0 / 510.0);
| ^~~
gamma.h:23:15: warning: 'gam::B14' defined but not used [-Wunused-variable]
23 | static double B14 = ( 7.0 / 6.0);
| ^~~
gamma.h:22:15: warning: 'gam::B12' defined but not used [-Wunused-variable]
22 | static double B12 = (-691.0 / 2730.0);
| ^~~
gamma.h:21:15: warning: 'gam::B10' defined but not used [-Wunused-variable]
21 | static double B10 = ( 5.0 / 66.0);
| ^~~
gamma.h:20:15: warning: 'gam::B8' defined but not used [-Wunused-variable]
20 | static double B8 = (-1.0 / 30.0);
| ^~
gamma.h:19:15: warning: 'gam::B6' defined but not used [-Wunused-variable]
19 | static double B6 = ( 1.0 / 42.0);
| ^~
gamma.h:18:15: warning: 'gam::B4' defined but not used [-Wunused-variable]
18 | static double B4 = (-1.0 / 30.0);
| ^~
gamma.h:17:15: warning: 'gam::B2' defined but not used [-Wunused-variable]
17 | static double B2 = ( 1.0 / 6.0);
| ^~
gamma.h:14:12: warning: 'gam::N' defined but not used [-Wunused-variable]
14 | static int N = 8;
| ^
gamma.h:11:15: warning: 'gam::LOG_PI' defined but not used [-Wunused-variable]
11 | static double LOG_PI = 1.14472988584940017; // log(pi)
| ^~~~~~
gamma.h:10:15: warning: 'gam::LOG_2PI' defined but not used [-Wunused-variable]
10 | static double LOG_2PI = 1.83787706640934548;
| ^~~~~~~
gamma.h:9:15: warning: 'gam::PI' defined but not used [-Wunused-variable]
9 | static double PI = 3.14159265358979324; // pi
| ^~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c emfit_phase_cf1.cpp -o emfit_phase_cf1.o
In file included from phase_gen.h:9,
from phase_cf1.h:5,
from emfit_phase_cf1.cpp:4:
unif.h: In instantiation of 'void _diag_::diag(const T1&, T2&, CSCMatrixT) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Vector<13>]':
unif.h:287:15: required from 'void diag(const T1&, T2&) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Vector<13>]'
287 | _diag_::diag(A, diag_index, typename matrix_category<T1>::type{});
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit_phase_cf1.cpp:30:7: required from here
30 | diag(Q, di);
| ~~~~^~~~~~~
unif.h:236:13: warning: unused variable 'm' [-Wunused-variable]
236 | const int m = traits1::nrow(A);
| ^
phase_gen.h: In instantiation of 'double estep(const GPH<T1, T2, T0>&, const PHGroupSample<T4, T5, T6>&, GPHEres<T7, T8>&, OptionT&, WorkSpace&) [with T0 = Rcpp::Vector<13>; T1 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T2 = S4matrix<CSCMatrixT>; T4 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T5 = Rcpp::Vector<13>; T6 = Rcpp::Vector<13>; T7 = std::vector<double>; T8 = S4matrix<CSCMatrixT>; OptionT = EMOptions; WorkSpace = GPHWorkSpace2]':
phase_cf1.h:121:15: required from 'double estep(const CF1<T1, GPHT>&, const DataT&, EresT&, OptionT&, WorkSpace&) [with T1 = Rcpp::Vector<14, Rcpp::PreserveStorage>; GPHT = GPH<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<CSCMatrixT>, Rcpp::Vector<13> >; DataT = PHGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; EresT = GPHEres<std::vector<double>, S4matrix<CSCMatrixT> >; OptionT = EMOptions; WorkSpace = GPHWorkSpace2]'
121 | return estep(model.gph, data, eres, options, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit.h:56:19: required from 'void emfit(ModelT&, const DataT&, OptionT&, ET&, WorkSpace&) [with ModelT = CF1<Rcpp::Vector<14, Rcpp::PreserveStorage>, GPH<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<CSCMatrixT>, Rcpp::Vector<13> > >; DataT = PHGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; OptionT = EMOptions; ET = GPHEres<std::vector<double>, S4matrix<CSCMatrixT> >; WorkSpace = GPHWorkSpace2]'
56 | prev_llf = estep(model, data, eres, options, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit_phase_cf1.cpp:131:8: required from here
131 | emfit(model, dat, opts, eres, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase_gen.h:230:10: warning: unused variable 'scale' [-Wunused-variable]
230 | double scale;
| ^~~~~
phase_gen.h:232:10: warning: unused variable 'tllf' [-Wunused-variable]
232 | double tllf = 0.0;
| ^~~~
phase_gen.h: In instantiation of 'double estep(const GPHPoi<GPH<T1, T2, T0> >&, const PHGroupSample<T4, T5, T6>&, GPHEres<T7, T8>&, OptionT&, WorkSpace&) [with T0 = Rcpp::Vector<13>; T1 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T2 = S4matrix<CSCMatrixT>; T4 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T5 = Rcpp::Vector<13>; T6 = Rcpp::Vector<13>; T7 = std::vector<double>; T8 = S4matrix<CSCMatrixT>; OptionT = EMOptions; WorkSpace = GPHWorkSpace2]':
phase_cf1.h:121:15: required from 'double estep(const CF1<T1, GPHT>&, const DataT&, EresT&, OptionT&, WorkSpace&) [with T1 = Rcpp::Vector<14, Rcpp::PreserveStorage>; GPHT = GPHPoi<GPH<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<CSCMatrixT>, Rcpp::Vector<13> > >; DataT = PHGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; EresT = GPHEres<std::vector<double>, S4matrix<CSCMatrixT> >; OptionT = EMOptions; WorkSpace = GPHWorkSpace2]'
121 | return estep(model.gph, data, eres, options, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit.h:56:19: required from 'void emfit(ModelT&, const DataT&, OptionT&, ET&, WorkSpace&) [with ModelT = CF1<Rcpp::Vector<14, Rcpp::PreserveStorage>, GPHPoi<GPH<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<CSCMatrixT>, Rcpp::Vector<13> > > >; DataT = PHGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; OptionT = EMOptions; ET = GPHEres<std::vector<double>, S4matrix<CSCMatrixT> >; WorkSpace = GPHWorkSpace2]'
56 | prev_llf = estep(model, data, eres, options, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit_phase_cf1.cpp:202:8: required from here
202 | emfit(model, dat, opts, eres, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase_gen.h:443:10: warning: unused variable 'scale' [-Wunused-variable]
443 | double scale;
| ^~~~~
phase_gen.h:445:10: warning: unused variable 'tllf' [-Wunused-variable]
445 | double tllf = 0.0;
| ^~~~
In file included from phase_gen.h:8:
blas.h: In instantiation of 'void _mcopy_::mcopy(const T1&, T2&, CSCMatrixT, DenseMatrixT) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Matrix<14>]':
blas.h:165:17: required from 'void mcopy(const T1&, T2&) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Matrix<14>]'
165 | _mcopy_::mcopy(
| ~~~~~~~~~~~~~~^
166 | A, B,
| ~~~~~
167 | typename matrix_category<T1>::type{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
168 | typename matrix_category<T2>::type{});
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blas.h:1374:8: required from 'int _gesv_::gesv(TRANS, double, const T1&, const T2&, T3&, CSCMatrixT) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T3 = std::vector<double>]'
1374 | mcopy(A, tmpA);
| ~~~~~^~~~~~~~~
blas.h:1403:22: required from 'int gesv(const T0&, double, const T1&, const T2&, T3&) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T3 = std::vector<double>; T0 = TRANS]'
1403 | return _gesv_::gesv(tr, alpha, A, B, C,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
1404 | typename matrix_category<T1>::type{});
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase_gen.h:209:7: required from 'double estep(const GPH<T1, T2, T0>&, const PHGroupSample<T4, T5, T6>&, GPHEres<T7, T8>&, OptionT&, WorkSpace&) [with T0 = Rcpp::Vector<13>; T1 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T2 = S4matrix<CSCMatrixT>; T4 = Rcpp::Vector<14, Rcpp::PreserveStorage>; T5 = Rcpp::Vector<13>; T6 = Rcpp::Vector<13>; T7 = std::vector<double>; T8 = S4matrix<CSCMatrixT>; OptionT = EMOptions; WorkSpace = GPHWorkSpace2]'
209 | gesv(TRANS{}, -1.0, model.Q, model.alpha, baralpha);
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase_cf1.h:121:15: required from 'double estep(const CF1<T1, GPHT>&, const DataT&, EresT&, OptionT&, WorkSpace&) [with T1 = Rcpp::Vector<14, Rcpp::PreserveStorage>; GPHT = GPH<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<CSCMatrixT>, Rcpp::Vector<13> >; DataT = PHGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; EresT = GPHEres<std::vector<double>, S4matrix<CSCMatrixT> >; OptionT = EMOptions; WorkSpace = GPHWorkSpace2]'
121 | return estep(model.gph, data, eres, options, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit.h:56:19: required from 'void emfit(ModelT&, const DataT&, OptionT&, ET&, WorkSpace&) [with ModelT = CF1<Rcpp::Vector<14, Rcpp::PreserveStorage>, GPH<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<CSCMatrixT>, Rcpp::Vector<13> > >; DataT = PHGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; OptionT = EMOptions; ET = GPHEres<std::vector<double>, S4matrix<CSCMatrixT> >; WorkSpace = GPHWorkSpace2]'
56 | prev_llf = estep(model, data, eres, options, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit_phase_cf1.cpp:131:8: required from here
131 | emfit(model, dat, opts, eres, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blas.h:116:13: warning: unused variable 'm' [-Wunused-variable]
116 | const int m = traits1::nrow(A);
| ^
In file included from phase_gen.h:7:
gamma.h:24:15: warning: 'gam::B16' defined but not used [-Wunused-variable]
24 | static double B16 = (-3617.0 / 510.0);
| ^~~
gamma.h:23:15: warning: 'gam::B14' defined but not used [-Wunused-variable]
23 | static double B14 = ( 7.0 / 6.0);
| ^~~
gamma.h:22:15: warning: 'gam::B12' defined but not used [-Wunused-variable]
22 | static double B12 = (-691.0 / 2730.0);
| ^~~
gamma.h:21:15: warning: 'gam::B10' defined but not used [-Wunused-variable]
21 | static double B10 = ( 5.0 / 66.0);
| ^~~
gamma.h:20:15: warning: 'gam::B8' defined but not used [-Wunused-variable]
20 | static double B8 = (-1.0 / 30.0);
| ^~
gamma.h:19:15: warning: 'gam::B6' defined but not used [-Wunused-variable]
19 | static double B6 = ( 1.0 / 42.0);
| ^~
gamma.h:18:15: warning: 'gam::B4' defined but not used [-Wunused-variable]
18 | static double B4 = (-1.0 / 30.0);
| ^~
gamma.h:17:15: warning: 'gam::B2' defined but not used [-Wunused-variable]
17 | static double B2 = ( 1.0 / 6.0);
| ^~
gamma.h:14:12: warning: 'gam::N' defined but not used [-Wunused-variable]
14 | static int N = 8;
| ^
gamma.h:11:15: warning: 'gam::LOG_PI' defined but not used [-Wunused-variable]
11 | static double LOG_PI = 1.14472988584940017; // log(pi)
| ^~~~~~
gamma.h:10:15: warning: 'gam::LOG_2PI' defined but not used [-Wunused-variable]
10 | static double LOG_2PI = 1.83787706640934548;
| ^~~~~~~
gamma.h:9:15: warning: 'gam::PI' defined but not used [-Wunused-variable]
9 | static double PI = 3.14159265358979324; // pi
| ^~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c emfit_phase_herlang.cpp -o emfit_phase_herlang.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c emfit_map_gen.cpp -o emfit_map_gen.o
In file included from emfit_phase_herlang.cpp:4:
phase_herlang.h: In instantiation of 'void mstep(const HErlangEres<V2>&, HErlang<T1, T2>&, OptionT) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; I = Rcpp::Vector<13>; V2 = std::vector<double>; OptionT = EMOptions]':
emfit.h:60:8: required from 'void emfit(ModelT&, const DataT&, OptionT&, ET&, WorkSpace&) [with ModelT = HErlang<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13> >; DataT = PHWeightSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage> >; OptionT = EMOptions; ET = HErlangEres<std::vector<double> >; WorkSpace = HErlangWorkSpace1]'
60 | mstep(eres, model, options);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
emfit_phase_herlang.cpp:37:8: required from here
37 | emfit(model, dat, opts, eres, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase_herlang.h:356:11: warning: unused variable 'alpha' [-Wunused-variable]
356 | double* alpha = trait2::value(model.alpha);
| ^~~~~
phase_herlang.h: In instantiation of 'void mstep(const HErlangEres<V2>&, HErlangPoi<T1, T2>&, OptionT) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; I = Rcpp::Vector<13>; V2 = std::vector<double>; OptionT = EMOptions]':
emfit.h:60:8: required from 'void emfit(ModelT&, const DataT&, OptionT&, ET&, WorkSpace&) [with ModelT = HErlangPoi<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13> >; DataT = PHGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; OptionT = EMOptions; ET = HErlangEres<std::vector<double> >; WorkSpace = HErlangWorkSpace2]'
60 | mstep(eres, model, options);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
emfit_phase_herlang.cpp:126:8: required from here
126 | emfit(model, dat, opts, eres, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase_herlang.h:378:11: warning: unused variable 'alpha' [-Wunused-variable]
378 | double* alpha = trait2::value(model.alpha);
| ^~~~~
In file included from phase_herlang.h:6:
gamma.h:24:15: warning: 'gam::B16' defined but not used [-Wunused-variable]
24 | static double B16 = (-3617.0 / 510.0);
| ^~~
gamma.h:23:15: warning: 'gam::B14' defined but not used [-Wunused-variable]
23 | static double B14 = ( 7.0 / 6.0);
| ^~~
gamma.h:22:15: warning: 'gam::B12' defined but not used [-Wunused-variable]
22 | static double B12 = (-691.0 / 2730.0);
| ^~~
gamma.h:21:15: warning: 'gam::B10' defined but not used [-Wunused-variable]
21 | static double B10 = ( 5.0 / 66.0);
| ^~~
gamma.h:20:15: warning: 'gam::B8' defined but not used [-Wunused-variable]
20 | static double B8 = (-1.0 / 30.0);
| ^~
gamma.h:19:15: warning: 'gam::B6' defined but not used [-Wunused-variable]
19 | static double B6 = ( 1.0 / 42.0);
| ^~
gamma.h:18:15: warning: 'gam::B4' defined but not used [-Wunused-variable]
18 | static double B4 = (-1.0 / 30.0);
| ^~
gamma.h:17:15: warning: 'gam::B2' defined but not used [-Wunused-variable]
17 | static double B2 = ( 1.0 / 6.0);
| ^~
gamma.h:14:12: warning: 'gam::N' defined but not used [-Wunused-variable]
14 | static int N = 8;
| ^
gamma.h:11:15: warning: 'gam::LOG_PI' defined but not used [-Wunused-variable]
11 | static double LOG_PI = 1.14472988584940017; // log(pi)
| ^~~~~~
gamma.h:10:15: warning: 'gam::LOG_2PI' defined but not used [-Wunused-variable]
10 | static double LOG_2PI = 1.83787706640934548;
| ^~~~~~~
gamma.h:9:15: warning: 'gam::PI' defined but not used [-Wunused-variable]
9 | static double PI = 3.14159265358979324; // pi
| ^~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c emfit_map_erhmm.cpp -o emfit_map_erhmm.o
In file included from map_gen.h:10,
from emfit_map_gen.cpp:4:
unif.h: In instantiation of 'void _diag_::diag(const T1&, T2&, DenseMatrixT) [with T1 = S4matrix<DenseMatrixT>; T2 = Rcpp::Vector<13>]':
unif.h:287:15: required from 'void diag(const T1&, T2&) [with T1 = S4matrix<DenseMatrixT>; T2 = Rcpp::Vector<13>]'
287 | _diag_::diag(A, diag_index, typename matrix_category<T1>::type{});
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit_map_gen.cpp:42:7: required from here
42 | diag(D0, di);
| ~~~~^~~~~~~~
unif.h:193:13: warning: unused variable 'm' [-Wunused-variable]
193 | const int m = traits1::nrow(A);
| ^
map_gen.h: In instantiation of 'void _mstep_::mstep(const MAPEres<Ev, Em>&, MAP<Mv, Mm, Mi>&, OptionT&, DenseMatrixT) [with Ev = Rcpp::Vector<14, Rcpp::PreserveStorage>; Em = S4matrix<DenseMatrixT>; Mv = Rcpp::Vector<14, Rcpp::PreserveStorage>; Mm = S4matrix<DenseMatrixT>; Mi = Rcpp::Vector<13>; OptionT = EMOptions]':
map_gen.h:428:17: required from 'void mstep(const MAPEres<Ev, Em>&, MAP<Mv, Mm, Mi>&, OptionT&) [with Ev = Rcpp::Vector<14, Rcpp::PreserveStorage>; Em = S4matrix<DenseMatrixT>; Mv = Rcpp::Vector<14, Rcpp::PreserveStorage>; Mm = S4matrix<DenseMatrixT>; Mi = Rcpp::Vector<13>; OptionT = EMOptions]'
428 | _mstep_::mstep(eres, model, options, typename matrix_category<Mm>::type{});
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit.h:60:8: required from 'void emfit(ModelT&, const DataT&, OptionT&, ET&, WorkSpace&) [with ModelT = MAP<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<DenseMatrixT>, Rcpp::Vector<13> >; DataT = MAPGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; OptionT = EMOptions; ET = MAPEres<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<DenseMatrixT> >; WorkSpace = MAPWorkSpace1<S4matrix<DenseMatrixT> >]'
60 | mstep(eres, model, options);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
emfit_map_gen.cpp:73:8: required from here
73 | emfit(model, dat, opts, eres, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
map_gen.h:256:17: warning: unused variable 'eb' [-Wunused-variable]
256 | const double* eb = stride_vector_traits<Ev>::value(eres.eb);
| ^~
map_gen.h:262:11: warning: unused variable 'alpha' [-Wunused-variable]
262 | double* alpha = stride_vector_traits<Mv>::value(model.alpha);
| ^~~~~
In file included from map_gen.h:7:
gamma.h:24:15: warning: 'gam::B16' defined but not used [-Wunused-variable]
24 | static double B16 = (-3617.0 / 510.0);
| ^~~
gamma.h:23:15: warning: 'gam::B14' defined but not used [-Wunused-variable]
23 | static double B14 = ( 7.0 / 6.0);
| ^~~
gamma.h:22:15: warning: 'gam::B12' defined but not used [-Wunused-variable]
22 | static double B12 = (-691.0 / 2730.0);
| ^~~
gamma.h:21:15: warning: 'gam::B10' defined but not used [-Wunused-variable]
21 | static double B10 = ( 5.0 / 66.0);
| ^~~
gamma.h:20:15: warning: 'gam::B8' defined but not used [-Wunused-variable]
20 | static double B8 = (-1.0 / 30.0);
| ^~
gamma.h:19:15: warning: 'gam::B6' defined but not used [-Wunused-variable]
19 | static double B6 = ( 1.0 / 42.0);
| ^~
gamma.h:18:15: warning: 'gam::B4' defined but not used [-Wunused-variable]
18 | static double B4 = (-1.0 / 30.0);
| ^~
gamma.h:17:15: warning: 'gam::B2' defined but not used [-Wunused-variable]
17 | static double B2 = ( 1.0 / 6.0);
| ^~
gamma.h:14:12: warning: 'gam::N' defined but not used [-Wunused-variable]
14 | static int N = 8;
| ^
gamma.h:11:15: warning: 'gam::LOG_PI' defined but not used [-Wunused-variable]
11 | static double LOG_PI = 1.14472988584940017; // log(pi)
| ^~~~~~
gamma.h:10:15: warning: 'gam::LOG_2PI' defined but not used [-Wunused-variable]
10 | static double LOG_2PI = 1.83787706640934548;
| ^~~~~~~
gamma.h:9:15: warning: 'gam::PI' defined but not used [-Wunused-variable]
9 | static double PI = 3.14159265358979324; // pi
| ^~
In file included from emfit_map_erhmm.cpp:4:
map_erhmm.h: In instantiation of 'void _mstep_::mstep(const ErlangHMMEres<Ev, Em>&, ErlangHMM<Tv, Ti, Tm>&, OptionT, DenseMatrixT) [with Ev = Rcpp::Vector<14, Rcpp::PreserveStorage>; Em = S4matrix<DenseMatrixT>; Tv = Rcpp::Vector<14, Rcpp::PreserveStorage>; Ti = Rcpp::Vector<13>; Tm = S4matrix<DenseMatrixT>; OptionT = EMOptions]':
map_erhmm.h:150:17: required from 'void mstep(const ErlangHMMEres<Ev, Em>&, ErlangHMM<Tv, Ti, Tm>&, OptionT&) [with Ev = Rcpp::Vector<14, Rcpp::PreserveStorage>; Em = S4matrix<DenseMatrixT>; Tv = Rcpp::Vector<14, Rcpp::PreserveStorage>; Ti = Rcpp::Vector<13>; Tm = S4matrix<DenseMatrixT>; OptionT = EMOptions]'
150 | _mstep_::mstep(eres, model, options, typename matrix_category<Tm>::type{});
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit.h:60:8: required from 'void emfit(ModelT&, const DataT&, OptionT&, ET&, WorkSpace&) [with ModelT = ErlangHMM<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, S4matrix<DenseMatrixT> >; DataT = MAPTimeSample<Rcpp::Vector<14, Rcpp::PreserveStorage> >; OptionT = EMOptions; ET = ErlangHMMEres<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<DenseMatrixT> >; WorkSpace = ErlangHMMWorkSpace1<S4matrix<DenseMatrixT> >]'
60 | mstep(eres, model, options);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
emfit_map_erhmm.cpp:51:8: required from here
51 | emfit(model, dat, opts, eres, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
map_erhmm.h:114:17: warning: unused variable 'eb' [-Wunused-variable]
114 | const double* eb = stride_vector_traits<Ev>::value(eres.eb);
| ^~
In file included from map_erhmm.h:8:
gamma.h:24:15: warning: 'gam::B16' defined but not used [-Wunused-variable]
24 | static double B16 = (-3617.0 / 510.0);
| ^~~
gamma.h:23:15: warning: 'gam::B14' defined but not used [-Wunused-variable]
23 | static double B14 = ( 7.0 / 6.0);
| ^~~
gamma.h:22:15: warning: 'gam::B12' defined but not used [-Wunused-variable]
22 | static double B12 = (-691.0 / 2730.0);
| ^~~
gamma.h:21:15: warning: 'gam::B10' defined but not used [-Wunused-variable]
21 | static double B10 = ( 5.0 / 66.0);
| ^~~
gamma.h:20:15: warning: 'gam::B8' defined but not used [-Wunused-variable]
20 | static double B8 = (-1.0 / 30.0);
| ^~
gamma.h:19:15: warning: 'gam::B6' defined but not used [-Wunused-variable]
19 | static double B6 = ( 1.0 / 42.0);
| ^~
gamma.h:18:15: warning: 'gam::B4' defined but not used [-Wunused-variable]
18 | static double B4 = (-1.0 / 30.0);
| ^~
gamma.h:17:15: warning: 'gam::B2' defined but not used [-Wunused-variable]
17 | static double B2 = ( 1.0 / 6.0);
| ^~
gamma.h:14:12: warning: 'gam::N' defined but not used [-Wunused-variable]
14 | static int N = 8;
| ^
gamma.h:11:15: warning: 'gam::LOG_PI' defined but not used [-Wunused-variable]
11 | static double LOG_PI = 1.14472988584940017; // log(pi)
| ^~~~~~
gamma.h:10:15: warning: 'gam::LOG_2PI' defined but not used [-Wunused-variable]
10 | static double LOG_2PI = 1.83787706640934548;
| ^~~~~~~
gamma.h:9:15: warning: 'gam::PI' defined but not used [-Wunused-variable]
9 | static double PI = 3.14159265358979324; // pi
| ^~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c emfit_map_gmmpp.cpp -o emfit_map_gmmpp.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c gth.cpp -o gth.o
emfit_map_gmmpp.cpp: In function 'Rcpp::List emfit_gmmpp_group(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::S4, Rcpp::S4, Rcpp::List, Rcpp::List, Rcpp::S4, Rcpp::S4, Rcpp::S4, Rcpp::S4, Rcpp::S4, Rcpp::S4, Rcpp::S4, Rcpp::S4, Rcpp::S4, Rcpp::S4)':
emfit_map_gmmpp.cpp:63:8: warning: unused variable 'm' [-Wunused-variable]
63 | auto m = tdat.length();
| ^
In file included from map_gmmpp.h:8,
from emfit_map_gmmpp.cpp:4:
unif.h: In instantiation of 'void _diag_::diag(const T1&, T2&, DenseMatrixT) [with T1 = S4matrix<DenseMatrixT>; T2 = Rcpp::Vector<13>]':
unif.h:287:15: required from 'void diag(const T1&, T2&) [with T1 = S4matrix<DenseMatrixT>; T2 = Rcpp::Vector<13>]'
287 | _diag_::diag(A, diag_index, typename matrix_category<T1>::type{});
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit_map_gmmpp.cpp:50:7: required from here
50 | diag(D0, di);
| ~~~~^~~~~~~~
unif.h:193:13: warning: unused variable 'm' [-Wunused-variable]
193 | const int m = traits1::nrow(A);
| ^
map_gmmpp.h: In instantiation of 'double estep(const GMMPP<MAP<Mv, Mm, Mi> >&, const MAPGroupSample<Gt, Gc, Gi>&, MAPEres<Ev, Em>&, OptionT&, WorkSpace&) [with Mv = Rcpp::Vector<14, Rcpp::PreserveStorage>; Mm = S4matrix<DenseMatrixT>; Mi = Rcpp::Vector<13>; Gt = Rcpp::Vector<14, Rcpp::PreserveStorage>; Gc = Rcpp::Vector<13>; Gi = Rcpp::Vector<13>; Ev = Rcpp::Vector<14, Rcpp::PreserveStorage>; Em = S4matrix<DenseMatrixT>; OptionT = EMOptions; WorkSpace = GMMPPWorkSpace<S4matrix<DenseMatrixT> >]':
emfit.h:56:19: required from 'void emfit(ModelT&, const DataT&, OptionT&, ET&, WorkSpace&) [with ModelT = GMMPP<MAP<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<DenseMatrixT>, Rcpp::Vector<13> > >; DataT = MAPGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; OptionT = EMOptions; ET = MAPEres<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<DenseMatrixT> >; WorkSpace = GMMPPWorkSpace<S4matrix<DenseMatrixT> >]'
56 | prev_llf = estep(model, data, eres, options, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit_map_gmmpp.cpp:82:8: required from here
82 | emfit(model, dat, opts, eres, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
map_gmmpp.h:174:16: warning: unused variable 'tmax' [-Wunused-variable]
174 | const double tmax = data.maxtime;
| ^~~~
map_gmmpp.h: In instantiation of 'void makeG(int, double, const MatT&, const MatT&, MatT&, const Tv&, const Tv&, Tv&, Tv&) [with MatT = S4matrix<DenseMatrixT>; Tv = std::vector<double>]':
map_gmmpp.h:217:10: required from 'double estep(const GMMPP<MAP<Mv, Mm, Mi> >&, const MAPGroupSample<Gt, Gc, Gi>&, MAPEres<Ev, Em>&, OptionT&, WorkSpace&) [with Mv = Rcpp::Vector<14, Rcpp::PreserveStorage>; Mm = S4matrix<DenseMatrixT>; Mi = Rcpp::Vector<13>; Gt = Rcpp::Vector<14, Rcpp::PreserveStorage>; Gc = Rcpp::Vector<13>; Gi = Rcpp::Vector<13>; Ev = Rcpp::Vector<14, Rcpp::PreserveStorage>; Em = S4matrix<DenseMatrixT>; OptionT = EMOptions; WorkSpace = GMMPPWorkSpace<S4matrix<DenseMatrixT> >]'
217 | makeG(GDAT(k), TDAT(k), model.map.D0, model.map.D1, G, inte_x, inte_w, inte_fx, inte_fv);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit.h:56:19: required from 'void emfit(ModelT&, const DataT&, OptionT&, ET&, WorkSpace&) [with ModelT = GMMPP<MAP<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<DenseMatrixT>, Rcpp::Vector<13> > >; DataT = MAPGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; OptionT = EMOptions; ET = MAPEres<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<DenseMatrixT> >; WorkSpace = GMMPPWorkSpace<S4matrix<DenseMatrixT> >]'
56 | prev_llf = estep(model, data, eres, options, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emfit_map_gmmpp.cpp:82:8: required from here
82 | emfit(model, dat, opts, eres, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
map_gmmpp.h:56:15: warning: variable 'dji' set but not used [-Wunused-but-set-variable]
56 | double dij, dji;
| ^~~
In file included from map_gmmpp.h:12:
map_gen.h: In instantiation of 'void _mstep_::mstep(const MAPEres<Ev, Em>&, MAP<Mv, Mm, Mi>&, OptionT&, DenseMatrixT) [with Ev = Rcpp::Vector<14, Rcpp::PreserveStorage>; Em = S4matrix<DenseMatrixT>; Mv = Rcpp::Vector<14, Rcpp::PreserveStorage>; Mm = S4matrix<DenseMatrixT>; Mi = Rcpp::Vector<13>; OptionT = EMOptions]':
map_gen.h:428:17: required from 'void mstep(const MAPEres<Ev, Em>&, MAP<Mv, Mm, Mi>&, OptionT&) [with Ev = Rcpp::Vector<14, Rcpp::PreserveStorage>; Em = S4matrix<DenseMatrixT>; Mv = Rcpp::Vector<14, Rcpp::PreserveStorage>; Mm = S4matrix<DenseMatrixT>; Mi = Rcpp::Vector<13>; OptionT = EMOptions]'
428 | _mstep_::mstep(eres, model, options, typename matrix_category<Mm>::type{});
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
map_gmmpp.h:285:8: required from 'void mstep(const MAPEres<Ev, Em>&, GMMPP<MAPT>&, OptionT&) [with Ev = Rcpp::Vector<14, Rcpp::PreserveStorage>; Em = S4matrix<DenseMatrixT>; MAPT = MAP<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<DenseMatrixT>, Rcpp::Vector<13> >; OptionT = EMOptions]'
285 | mstep(eres, model.map, options);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
emfit.h:60:8: required from 'void emfit(ModelT&, const DataT&, OptionT&, ET&, WorkSpace&) [with ModelT = GMMPP<MAP<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<DenseMatrixT>, Rcpp::Vector<13> > >; DataT = MAPGroupSample<Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13>, Rcpp::Vector<13> >; OptionT = EMOptions; ET = MAPEres<Rcpp::Vector<14, Rcpp::PreserveStorage>, S4matrix<DenseMatrixT> >; WorkSpace = GMMPPWorkSpace<S4matrix<DenseMatrixT> >]'
60 | mstep(eres, model, options);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
emfit_map_gmmpp.cpp:82:8: required from here
82 | emfit(model, dat, opts, eres, work);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
map_gen.h:256:17: warning: unused variable 'eb' [-Wunused-variable]
256 | const double* eb = stride_vector_traits<Ev>::value(eres.eb);
| ^~
map_gen.h:262:11: warning: unused variable 'alpha' [-Wunused-variable]
262 | double* alpha = stride_vector_traits<Mv>::value(model.alpha);
| ^~~~~
In file included from map_gmmpp.h:6:
gamma.h: At global scope:
gamma.h:24:15: warning: 'gam::B16' defined but not used [-Wunused-variable]
24 | static double B16 = (-3617.0 / 510.0);
| ^~~
gamma.h:23:15: warning: 'gam::B14' defined but not used [-Wunused-variable]
23 | static double B14 = ( 7.0 / 6.0);
| ^~~
gamma.h:22:15: warning: 'gam::B12' defined but not used [-Wunused-variable]
22 | static double B12 = (-691.0 / 2730.0);
| ^~~
gamma.h:21:15: warning: 'gam::B10' defined but not used [-Wunused-variable]
21 | static double B10 = ( 5.0 / 66.0);
| ^~~
gamma.h:20:15: warning: 'gam::B8' defined but not used [-Wunused-variable]
20 | static double B8 = (-1.0 / 30.0);
| ^~
gamma.h:19:15: warning: 'gam::B6' defined but not used [-Wunused-variable]
19 | static double B6 = ( 1.0 / 42.0);
| ^~
gamma.h:18:15: warning: 'gam::B4' defined but not used [-Wunused-variable]
18 | static double B4 = (-1.0 / 30.0);
| ^~
gamma.h:17:15: warning: 'gam::B2' defined but not used [-Wunused-variable]
17 | static double B2 = ( 1.0 / 6.0);
| ^~
gamma.h:14:12: warning: 'gam::N' defined but not used [-Wunused-variable]
14 | static int N = 8;
| ^
gamma.h:11:15: warning: 'gam::LOG_PI' defined but not used [-Wunused-variable]
11 | static double LOG_PI = 1.14472988584940017; // log(pi)
| ^~~~~~
gamma.h:10:15: warning: 'gam::LOG_2PI' defined but not used [-Wunused-variable]
10 | static double LOG_2PI = 1.83787706640934548;
| ^~~~~~~
gamma.h:9:15: warning: 'gam::PI' defined but not used [-Wunused-variable]
9 | static double PI = 3.14159265358979324; // pi
| ^~
In file included from gth.h:6,
from gth.cpp:4:
blas.h: In instantiation of 'void _mcopy_::mcopy(const T1&, T2&, CSCMatrixT, DenseMatrixT) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Matrix<14>]':
blas.h:165:17: required from 'void mcopy(const T1&, T2&) [with T1 = S4matrix<CSCMatrixT>; T2 = Rcpp::Matrix<14>]'
165 | _mcopy_::mcopy(
| ~~~~~~~~~~~~~~^
166 | A, B,
| ~~~~~
167 | typename matrix_category<T1>::type{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
168 | typename matrix_category<T2>::type{});
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gth.h:56:8: required from 'void markov_gth(const Tm&, Tv&) [with Tm = S4matrix<CSCMatrixT>; Tv = Rcpp::Vector<14, Rcpp::PreserveStorage>]'
56 | mcopy(Q, A);
| ~~~~~^~~~~~
gth.cpp:16:13: required from here
16 | markov_gth(Q, x);
| ~~~~~~~~~~^~~~~~
blas.h:116:13: warning: unused variable 'm' [-Wunused-variable]
116 | const int m = traits1::nrow(A);
| ^
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -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 -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/mapfit/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/mapfit/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/mapfit/src'
installing to /data/gannet/ripley/R/packages/tests-devel/mapfit.Rcheck/00LOCK-mapfit/00new/mapfit/libs
** 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)