Install log for 'hmcdm'

* installing *source* package ‘hmcdm’ ...
** package ‘hmcdm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/hmcdm/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'/data/gannet/ripley/R/test-dev/progress/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 RcppExports.cpp -o RcppExports.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'/data/gannet/ripley/R/test-dev/progress/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 basic_functions.cpp -o basic_functions.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'/data/gannet/ripley/R/test-dev/progress/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 extract_functions.cpp -o extract_functions.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'/data/gannet/ripley/R/test-dev/progress/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 mcmc_functions.cpp -o mcmc_functions.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'/data/gannet/ripley/R/test-dev/progress/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 resp_functions.cpp -o resp_functions.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'/data/gannet/ripley/R/test-dev/progress/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 rt_functions.cpp -o rt_functions.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'/data/gannet/ripley/R/test-dev/progress/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 trans_functions.cpp -o trans_functions.o
trans_functions.cpp: In function 'arma::cube sim_alphas(std::string, Rcpp::Nullable<arma::Col<double>&>, Rcpp::Nullable<arma::Col<double>&>, Rcpp::Nullable<arma::Mat<double>&>, Rcpp::Nullable<arma::Cube<double>&>, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double>&>, int, int, Rcpp::Nullable<arma::Mat<double>&>, Rcpp::Nullable<arma::Mat<double> >)':
trans_functions.cpp:532:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  532 |     for(unsigned int i=0; i<N; i++){
      |                           ~^~
mcmc_functions.cpp: In function 'Rcpp::List parm_update_HO_RT_joint_g(const arma::cube&, arma::cube&, arma::vec&, arma::vec&, arma::vec&, arma::cube, arma::mat&, arma::vec&, arma::vec&, arma::mat&, arma::cube, arma::mat&, arma::mat, Rcpp::List, int, double, arma::mat, double, arma::vec, double, double)':
mcmc_functions.cpp:1178:36: warning: 't_star' may be used uninitialized [-Wmaybe-uninitialized]
 1178 |       Gs.row(i) = G2vec_efficient_g(ETA,J_incidence,alphas.subcube(i,0,0,i,(K-1),(T-1)),
      |                   ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1179 |              t_star,Q_matrix,Design_array,i).t();
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mcmc_functions.cpp:1145:61: note: 't_star' was declared here
 1145 |   double a_alpha, scl_alpha, mu_gamma, sd_gamma, alpha_sqr, t_star;
      |                                                             ^~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:661,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
                 from trans_functions.cpp:1:
In constructor 'arma::Mat<eT>::Mat(arma::uword, arma::uword) [with eT = double]',
    inlined from 'arma::cube sim_alphas(std::string, Rcpp::Nullable<arma::Col<double>&>, Rcpp::Nullable<arma::Col<double>&>, Rcpp::Nullable<arma::Mat<double>&>, Rcpp::Nullable<arma::Cube<double>&>, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double>&>, int, int, Rcpp::Nullable<arma::Mat<double>&>, Rcpp::Nullable<arma::Mat<double> >)' at trans_functions.cpp:529:24:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:65:21: warning: 'K' may be used uninitialized [-Wmaybe-uninitialized]
   65 |   , n_elem(in_n_rows*in_n_cols)
      |            ~~~~~~~~~^~~~~~~~~~
trans_functions.cpp: In function 'arma::cube sim_alphas(std::string, Rcpp::Nullable<arma::Col<double>&>, Rcpp::Nullable<arma::Col<double>&>, Rcpp::Nullable<arma::Mat<double>&>, Rcpp::Nullable<arma::Cube<double>&>, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double>&>, int, int, Rcpp::Nullable<arma::Mat<double>&>, Rcpp::Nullable<arma::Mat<double> >)':
trans_functions.cpp:507:16: note: 'K' was declared here
  507 |   unsigned int K;
      |                ^
mcmc_functions.cpp: In function 'Rcpp::List parm_update_HO_RT_sep_g(arma::cube, arma::cube&, arma::vec&, arma::vec&, arma::vec&, arma::cube, arma::mat&, arma::vec&, arma::vec&, arma::vec&, arma::cube, arma::mat&, arma::mat, Rcpp::List, int, double, double, double, arma::vec, double, double)':
mcmc_functions.cpp:637:36: warning: 't_star' may be used uninitialized [-Wmaybe-uninitialized]
  637 |       Gs.row(i) = G2vec_efficient_g(ETA,J_incidence,alphas.subcube(i,0,0,i,(K-1),(T-1)),
      |                   ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  638 |                t_star,Q_matrix,Design_array,i).t();
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mcmc_functions.cpp:606:61: note: 't_star' was declared here
  606 |   double a_alpha, scl_alpha, mu_gamma, sd_gamma, alpha_sqr, t_star;
      |                                                             ^~~~~~
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 hmcdm.so RcppExports.o basic_functions.o extract_functions.o mcmc_functions.o resp_functions.o rt_functions.o trans_functions.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/hmcdm/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/hmcdm/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/hmcdm/src'
installing to /data/gannet/ripley/R/packages/tests-devel/hmcdm.Rcheck/00LOCK-hmcdm/00new/hmcdm/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (hmcdm)