Install log for 'surveyvoi'

* installing *source* package ‘surveyvoi’ ...
** package ‘surveyvoi’ successfully unpacked and MD5 sums checked
** using staged installation
checking if R found... yes
configure: R version: 4.5.0
checking for pkg-config... yes
configure: Package PKG_CPPFLAGS: -I/usr/local/include  
configure: Package PKG_LIBS:      -lgmpxx -lgmp  -lmpfr -lgmp 
checking if gmp compiles... yes
checking if mpfr compiles... yes
configure: configuration successful!
configure: creating ./config.status
config.status: creating src/Makevars
** 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/surveyvoi/src'
rm -f surveyvoi.so RcppExports.o functions.o init.o rcpp_approx_expected_value_of_decision_given_survey_scheme.o rcpp_expected_value_of_action.o rcpp_expected_value_of_decision_given_current_info.o rcpp_expected_value_of_decision_given_survey_scheme.o rcpp_feasible_actions_ilp_matrix.o rcpp_heuristic_prioritization.o rcpp_model_performance.o rcpp_pmedian_constraint_matrix.o rcpp_probability.o rcpp_sample_states.o rcpp_states.o rcpp_update_posterior_probability_matrix.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 functions.cpp -o functions.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/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 init.c -o init.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 rcpp_approx_expected_value_of_decision_given_survey_scheme.cpp -o rcpp_approx_expected_value_of_decision_given_survey_scheme.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 rcpp_expected_value_of_action.cpp -o rcpp_expected_value_of_action.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 rcpp_expected_value_of_decision_given_current_info.cpp -o rcpp_expected_value_of_decision_given_current_info.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 rcpp_expected_value_of_decision_given_survey_scheme.cpp -o rcpp_expected_value_of_decision_given_survey_scheme.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 rcpp_feasible_actions_ilp_matrix.cpp -o rcpp_feasible_actions_ilp_matrix.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 rcpp_heuristic_prioritization.cpp -o rcpp_heuristic_prioritization.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 rcpp_model_performance.cpp -o rcpp_model_performance.o
rcpp_expected_value_of_decision_given_survey_scheme.cpp: In function 'double rcpp_expected_value_of_decision_given_survey_scheme(Eigen::MatrixXd, std::vector<bool>, Eigen::VectorXd, Eigen::VectorXd, std::vector<bool>, Eigen::VectorXd, Eigen::VectorXd, Eigen::VectorXd, Eigen::VectorXd, Eigen::VectorXi, double)':
rcpp_expected_value_of_decision_given_survey_scheme.cpp:37:21: warning: unused variable 'n_f_outcomes' [-Wunused-variable]
   37 |   const std::size_t n_f_outcomes = n_states(n_pu_surveyed_in_scheme) + 1;
      |                     ^~~~~~~~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 rcpp_pmedian_constraint_matrix.cpp -o rcpp_pmedian_constraint_matrix.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 rcpp_probability.cpp -o rcpp_probability.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 rcpp_sample_states.cpp -o rcpp_sample_states.o
rcpp_heuristic_prioritization.cpp: In function 'void greedy_heuristic_prioritization(Eigen::MatrixXd&, Eigen::VectorXd&, Eigen::VectorXd&, Eigen::VectorXd&, Eigen::VectorXi&, double, std::vector<bool>&)':
rcpp_heuristic_prioritization.cpp:10:21: warning: unused variable 'n_f' [-Wunused-variable]
   10 |   const std::size_t n_f = rij.rows();
      |                     ^~~
rcpp_heuristic_prioritization.cpp:33:10: warning: unused variable 'curr_cost' [-Wunused-variable]
   33 |   double curr_cost;
      |          ^~~~~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 rcpp_states.cpp -o rcpp_states.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include   -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/PoissonBinomial/include' -I'/data/gannet/ripley/R/test-dev/nloptr/include' -I/usr/local/include    -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 rcpp_update_posterior_probability_matrix.cpp -o rcpp_update_posterior_probability_matrix.o
In file included from /usr/local/gcc13/include/c++/13.2.0/vector:67,
                 from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:60,
                 from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27,
                 from package.h:11,
                 from rcpp_heuristic_prioritization.h:5,
                 from rcpp_heuristic_prioritization.cpp:1:
In member function 'std::vector<bool, _Alloc>::reference std::vector<bool, _Alloc>::operator[](size_type) [with _Alloc = std::allocator<bool>]',
    inlined from 'void greedy_heuristic_prioritization(Eigen::MatrixXd&, Eigen::VectorXd&, Eigen::VectorXd&, Eigen::VectorXd&, Eigen::VectorXi&, double, std::vector<bool>&)' at rcpp_heuristic_prioritization.cpp:107:22:
/usr/local/gcc13/include/c++/13.2.0/bits/stl_bvector.h:1050:23: warning: 'curr_idx' may be used uninitialized [-Wmaybe-uninitialized]
 1050 |       { return begin()[__n]; }
      |                ~~~~~~~^
rcpp_heuristic_prioritization.cpp: In function 'void greedy_heuristic_prioritization(Eigen::MatrixXd&, Eigen::VectorXd&, Eigen::VectorXd&, Eigen::VectorXd&, Eigen::VectorXi&, double, std::vector<bool>&)':
rcpp_heuristic_prioritization.cpp:35:15: note: 'curr_idx' was declared here
   35 |   std::size_t curr_idx;
      |               ^~~~~~~~
rcpp_pmedian_constraint_matrix.cpp: In function 'Rcpp::List rcpp_pmedian_constraint_matrix(Eigen::MatrixXd, Rcpp::NumericVector)':
rcpp_pmedian_constraint_matrix.cpp:8:15: warning: unused variable 'n_vars' [-Wunused-variable]
    8 |   std::size_t n_vars = n + (n * n);
      |               ^~~~~~
rcpp_sample_states.cpp: In function 'void sample_n_uniform_states_without_replacement(std::size_t, Eigen::MatrixXd&, std::vector<__gmp_expr<__mpz_struct [1], __mpz_struct [1]> >&)':
rcpp_sample_states.cpp:62:21: warning: unused variable 'n_v' [-Wunused-variable]
   62 |   const std::size_t n_v = pij.size();
      |                     ^~~
rcpp_sample_states.cpp: In function 'void sample_n_weighted_states_without_replacement(std::size_t, Eigen::MatrixXd&, std::vector<__gmp_expr<__mpz_struct [1], __mpz_struct [1]> >&)':
rcpp_sample_states.cpp:115:21: warning: unused variable 'n_v' [-Wunused-variable]
  115 |   const std::size_t n_v = pij.size();
      |                     ^~~
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 surveyvoi.so RcppExports.o functions.o init.o rcpp_approx_expected_value_of_decision_given_survey_scheme.o rcpp_expected_value_of_action.o rcpp_expected_value_of_decision_given_current_info.o rcpp_expected_value_of_decision_given_survey_scheme.o rcpp_feasible_actions_ilp_matrix.o rcpp_heuristic_prioritization.o rcpp_model_performance.o rcpp_pmedian_constraint_matrix.o rcpp_probability.o rcpp_sample_states.o rcpp_states.o rcpp_update_posterior_probability_matrix.o -lgmpxx -lgmp -lmpfr -lgmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/surveyvoi/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/surveyvoi/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/surveyvoi/src'
installing to /data/gannet/ripley/R/packages/tests-devel/surveyvoi.Rcheck/00LOCK-surveyvoi/00new/surveyvoi/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (surveyvoi)