* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘mapfit’ ...
** package ‘mapfit’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpdyYEnl/R.INSTALL274aac4c2ab100/mapfit/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phase_dist.cpp -o phase_dist.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
| ^~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c emfit_phase_gen.cpp -o emfit_phase_gen.o
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"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c emfit_phase_herlang.cpp -o emfit_phase_herlang.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"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c emfit_map_gen.cpp -o emfit_map_gen.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
| ^~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c emfit_map_erhmm.cpp -o emfit_map_erhmm.o
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"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c emfit_map_gmmpp.cpp -o emfit_map_gmmpp.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
| ^~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c gth.cpp -o gth.o
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"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -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/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpdyYEnl/R.INSTALL274aac4c2ab100/mapfit/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpdyYEnl/R.INSTALL274aac4c2ab100/mapfit/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpdyYEnl/R.INSTALL274aac4c2ab100/mapfit/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-mapfit/00new/mapfit/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘mapfit’
finding HTML links ... done
AERHMMClass html
AHerlangClass html
BCpAug89 html
CF1Class html
ERHMMClass html
GMMPPClass html
GPHClass html
HErlangClass html
MAPClass html
as.gph html
as.map html
cf1 html
cf1.param html
cf1.param.linear html
cf1.param.power html
ctmc.st html
data.frame.map.group html
data.frame.map.time html
data.frame.phase.group html
data.frame.phase.time html
dphase html
emoptions html
erhmm html
erhmm.param html
gmmpp html
gph.param html
herlang html
herlang.param html
map html
map.acf html
map.jmoment html
map.mmoment html
map.param html
mapfit-package html
mapfit.group html
mapfit.point html
mmpp html
ph html
ph.bidiag html
ph.coxian html
ph.mean html
ph.moment html
ph.tridiag html
ph.var html
phfit.3mom html
phfit.density html
phfit.group html
phfit.point html
pphase html
rphase html
*** 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)