* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘stpm’ ...
** package ‘stpm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmptqMohL/R.INSTALL2fc4a55ee18fed/stpm/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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c devlik.cpp -o devlik.o
devlik.cpp: In function ‘SEXPREC* devlik(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
devlik.cpp:459:13: warning: unused variable ‘t_n’ [-Wunused-variable]
459 | int t_n = m0_v.n_elem;
| ^~~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c devlik_g.cpp -o devlik_g.o
devlik_g.cpp: In function ‘SEXPREC* devlik_g(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
devlik_g.cpp:407:13: warning: unused variable ‘t_n’ [-Wunused-variable]
407 | int t_n = m0_v.n_elem;
| ^~~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c devlik_g_2.cpp -o devlik_g_2.o
devlik_g_2.cpp: In function ‘SEXPREC* devlik_g_2(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
devlik_g_2.cpp:362:13: warning: unused variable ‘t_n’ [-Wunused-variable]
362 | int t_n = m0_v.n_elem;
| ^~~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c hes_spm_g.cpp -o hes_spm_g.o
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c loglik.cpp -o loglik.o
loglik.cpp: In function ‘double f_j2(double, double, double, double, double, double, double, double, double, double)’:
loglik.cpp:26:16: warning: unused variable ‘c1’ [-Wunused-variable]
26 | double c1 = (u / (r0 - rs) + 2 * q)*exp(-1 * u*t0);
| ^~
loglik.cpp: In function ‘double f_i1(double, double, double, double, double, double, double, double, double, double, double)’:
loglik.cpp:42:16: warning: unused variable ‘c1’ [-Wunused-variable]
42 | double c1 = (u / (r0 - rs) + 2 * q)*exp((-1) * u*t0);
| ^~
loglik.cpp:43:16: warning: unused variable ‘w_u’ [-Wunused-variable]
43 | double w_u = (-1)*q*f + q*a*(f - f1) / sqrt(pow(a, 2) + 2 * q*pow(b, 2));
| ^~~
loglik.cpp: In function ‘double mu_int(double, double, double, double, double, double, double, double, double, double, double)’:
loglik.cpp:59:16: warning: unused variable ‘w_u’ [-Wunused-variable]
59 | double w_u = (-1)*q*f + q*a*(f - f1) / sqrt(pow(a, 2) + 2 * q*pow(b, 2));
| ^~~
loglik.cpp: In function ‘SEXPREC* mloglik(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
loglik.cpp:114:13: warning: unused variable ‘t_n’ [-Wunused-variable]
114 | int t_n = m0_v.n_elem;
| ^~~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c loglik_g.cpp -o loglik_g.o
loglik_g.cpp: In function ‘double f_j2_g(double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double)’:
loglik_g.cpp:34:16: warning: unused variable ‘c1’ [-Wunused-variable]
34 | double c1 = (u / (r0 - rs) + 2 * q)*exp(-1 * u*t0);
| ^~
loglik_g.cpp: In function ‘double f_i1_g(double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double)’:
loglik_g.cpp:55:16: warning: unused variable ‘c1’ [-Wunused-variable]
55 | double c1 = (u / (r0 - rs) + 2 * q)*exp((-1) * u*t0);
| ^~
loglik_g.cpp:56:16: warning: unused variable ‘w_u’ [-Wunused-variable]
56 | double w_u = (-1)*q*f + q*a*(f - f1) / sqrt(pow(a, 2) + 2 * q*pow(b, 2));
| ^~~
loglik_g.cpp: In function ‘double mu_int_g(double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double)’:
loglik_g.cpp:77:16: warning: unused variable ‘w_u’ [-Wunused-variable]
77 | double w_u = (-1)*q*f + q*a*(f - f1) / sqrt(pow(a, 2) + 2 * q*pow(b, 2));
| ^~~
loglik_g.cpp: In function ‘SEXPREC* mloglik_g(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
loglik_g.cpp:140:13: warning: unused variable ‘t_n’ [-Wunused-variable]
140 | int t_n = m0_v.n_elem;
| ^~~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c loglik_g_2.cpp -o loglik_g_2.o
loglik_g_2.cpp: In function ‘double f_j2_g_2(double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double)’:
loglik_g_2.cpp:35:16: warning: unused variable ‘c1’ [-Wunused-variable]
35 | double c1 = (u / (r0 - rs) + 2 * q)*exp(-1 * u*t0);
| ^~
loglik_g_2.cpp: In function ‘double f_i1_g_2(double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double)’:
loglik_g_2.cpp:58:16: warning: unused variable ‘c1’ [-Wunused-variable]
58 | double c1 = (u / (r0 - rs) + 2 * q)*exp((-1) * u*t0);
| ^~
loglik_g_2.cpp:59:16: warning: unused variable ‘w_u’ [-Wunused-variable]
59 | double w_u = (-1)*q*f + q*a*(f - f1) / sqrt(pow(a, 2) + 2 * q*pow(b, 2));
| ^~~
loglik_g_2.cpp: In function ‘double mu_int_g_2(double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double)’:
loglik_g_2.cpp:82:16: warning: unused variable ‘w_u’ [-Wunused-variable]
82 | double w_u = (-1)*q*f + q*a*(f - f1) / sqrt(pow(a, 2) + 2 * q*pow(b, 2));
| ^~~
loglik_g_2.cpp: In function ‘SEXPREC* mloglik_g_2(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
loglik_g_2.cpp:147:13: warning: unused variable ‘t_n’ [-Wunused-variable]
147 | int t_n = m0_v.n_elem;
| ^~~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c simdataND.cpp -o simdataND.o
simdataND.cpp: In function ‘SEXPREC* simdata_ND(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
simdataND.cpp:148:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
148 | for(int i=0; i<data.size(); i++) {
| ~^~~~~~~~~~~~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spm_1D.cpp -o spm_1D.o
spm_1D.cpp: In function ‘double mu(double, double, double, double, double, double, double, double)’:
spm_1D.cpp:23:15: warning: variable ‘hf1H’ set but not used [-Wunused-but-set-variable]
23 | double hfH, hf1H, mu0Ht, mu;
| ^~~~
spm_1D.cpp: In function ‘void ode45_simpson(double, double, double, double*, double&, double, double, double, double, double, double, double, double)’:
spm_1D.cpp:78:9: warning: variable ‘res’ set but not used [-Wunused-but-set-variable]
78 | int res = func1(k1ar, t,out, fH, f1H, aH, bH, QH, thetaH);
| ^~~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spm_discrete.cpp -o spm_discrete.o
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spm_integral_MD.cpp -o spm_integral_MD.o
spm_integral_MD.cpp: In function ‘SEXPREC* simCont(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
spm_integral_MD.cpp:423:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
423 | for(int i=0; i<data.size(); i++) {
| ~^~~~~~~~~~~~
spm_integral_MD.cpp: In function ‘SEXPREC* simGenCont(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
spm_integral_MD.cpp:905:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
905 | for(int i=0; i<data.size(); i++) {
| ~^~~~~~~~~~~~
spm_integral_MD.cpp:913:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
913 | for(int i=0; i<data.size(); i++) {
| ~^~~~~~~~~~~~
spm_integral_MD.cpp: In function ‘SEXPREC* complikGenNonGenetic(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
spm_integral_MD.cpp:1050:17: warning: variable ‘L1Y’ set but not used [-Wunused-but-set-variable]
1050 | long double L1Y, L1Q, L0Y, L0Q;
| ^~~
spm_integral_MD.cpp: In function ‘SEXPREC* simGenCont(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
spm_integral_MD.cpp:725:13: warning: ‘t1’ may be used uninitialized [-Wmaybe-uninitialized]
725 | t2 = t1 + Rcpp::runif(1,-1.0*dt/10,dt/10)[0] + dt;
spm_integral_MD.cpp:703:10: note: ‘t1’ was declared here
703 | double t1;
| ^~
spm_integral_MD.cpp: In function ‘SEXPREC* complikGenNonGenetic(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
spm_integral_MD.cpp:1189:16: warning: ‘L1’ may be used uninitialized [-Wmaybe-uninitialized]
1189 | L1 = L1*mu(t2, m21, gamma21, fH, f1H, mu0H, thetaH, QH)*exp(s1);
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spm_integral_MD.cpp:961:18: note: ‘L1’ was declared here
961 | long double L, L1, L0; // Likelihoods for carriers (1) and non-carriers (0)
| ^~
spm_integral_MD.cpp:1190:16: warning: ‘L0’ may be used uninitialized [-Wmaybe-uninitialized]
1190 | L0 = L0*mu(t2, m20, gamma20, fL, f1L, mu0L, thetaL, QL)*exp(s0);
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spm_integral_MD.cpp:961:22: note: ‘L0’ was declared here
961 | long double L, L1, L0; // Likelihoods for carriers (1) and non-carriers (0)
| ^~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spm_integral_md_linear.cpp -o spm_integral_md_linear.o
gcc-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stpm_init.c -o stpm_init.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o stpm.so devlik.o devlik_g.o devlik_g_2.o hes_spm_g.o loglik.o loglik_g.o loglik_g_2.o simdataND.o spm_1D.o spm_discrete.o spm_integral_MD.o spm_integral_md_linear.o stpm_init.o -fopenmp -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/RtmptqMohL/R.INSTALL2fc4a55ee18fed/stpm/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmptqMohL/R.INSTALL2fc4a55ee18fed/stpm/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmptqMohL/R.INSTALL2fc4a55ee18fed/stpm/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-stpm/00new/stpm/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘stpm’
finding HTML links ... done
LRTest html
assign_to_global html
ex_data html
func1 html
get.column.index html
getNextY.cont html
getNextY.cont2 html
getNextY.discr html
getNextY.discr.m html
getPrevY.discr html
getPrevY.discr.m html
longdat html
m html
make.short.format html
mu html
prepare_data html
prepare_data_cont html
prepare_data_discr html
sigma_sq html
sim_pobs html
simdata_cont html
simdata_discr html
simdata_gamma_frailty html
simdata_time_dep html
spm html
spm.impute html
spm_con_1d html
spm_con_1d_g html
spm_cont_lin html
spm_cont_quad_lin html
spm_continuous html
spm_discrete html
spm_pobs html
spm_projection html
spm_time_dep html
stpm html
trim html
trim.leading html
trim.trailing html
vitstat html
** building package indices
** installing vignettes
** 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 (stpm)