Install log for 'stpm'

* installing *source* package ‘stpm’ ...
** package ‘stpm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (GCC) 13.2.0’
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/stpm/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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   -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++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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   -c devlik_g.cpp -o devlik_g.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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   -c devlik_g_2.cpp -o devlik_g_2.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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   -c hes_spm_g.cpp -o hes_spm_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++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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   -c loglik.cpp -o loglik.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++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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   -c loglik_g.cpp -o loglik_g.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++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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   -c loglik_g_2.cpp -o loglik_g_2.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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   -c simdataND.cpp -o simdataND.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++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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   -c spm_1D.cpp -o spm_1D.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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   -c spm_discrete.cpp -o spm_discrete.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);
      |         ^~~
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++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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   -c spm_integral_MD.cpp -o spm_integral_MD.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++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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   -c spm_integral_md_linear.cpp -o spm_integral_md_linear.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c stpm_init.c -o stpm_init.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++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -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/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/stpm/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/stpm/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/stpm/src'
installing to /data/gannet/ripley/R/packages/tests-devel/stpm.Rcheck/00LOCK-stpm/00new/stpm/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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)