Install log for 'hmcdm'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘hmcdm’ ...
** this is package ‘hmcdm’ version ‘2.1.1’
** package ‘hmcdm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-15 (Debian 15.2.0-4) 15.2.0’
make[1]: Entering directory '/tmp/Rtmpge1T6A/R.INSTALL391666596be522/hmcdm/src'
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native   -c basic_functions.cpp -o basic_functions.o
basic_functions.cpp: In function ‘arma::mat ETAmat(unsigned int, unsigned int, const arma::mat&)’:
basic_functions.cpp:178:51: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::eGlue<arma::Glue<arma::Row<double>, arma::Col<double>, arma::glue_times>, arma::Glue<arma::Row<double>, arma::Op<arma::Row<double>, arma::op_htrans>, arma::glue_times>, arma::eglue_minus>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
  178 |       double compare = arma::conv_to<double>::from(qj*alpha_c - qj*qj.t());
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:496,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
                 from basic_functions.cpp:1:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native   -c extract_functions.cpp -o extract_functions.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native   -c mcmc_functions.cpp -o mcmc_functions.o
mcmc_functions.cpp: In function ‘void parm_update_rRUM_g(const arma::cube&, arma::cube&, arma::vec&, arma::vec&, const arma::mat&, arma::mat&, arma::vec&, arma::mat, const arma::cube&, arma::cube&, arma::mat&, arma::mat&, const arma::vec&)’:
mcmc_functions.cpp:1459:49: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
 1459 |         c_aik_1 = (arma::conv_to< double >::from( alpha_i_1.t()*bijectionvector(K) ));
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:496,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
                 from mcmc_functions.cpp:1:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
mcmc_functions.cpp:1462:49: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
 1462 |         c_aik_0 = (arma::conv_to< double >::from( alpha_i_0.t()*bijectionvector(K) ));
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
mcmc_functions.cpp:1549:57: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
 1549 |       double Sumalphak =  (arma::conv_to< double >::from(ak.t() * ak));
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
mcmc_functions.cpp:1550:53: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
 1550 |       double SumXjk = (arma::conv_to< double >::from(Xjk.t() * Xjk));
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
mcmc_functions.cpp:1551:59: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
 1551 |       double SumXjkalphak = (arma::conv_to< double >::from(Xjk.t() * ak));
      |                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
mcmc_functions.cpp: In function ‘void parm_update_NIDA_indept_g(const arma::cube&, arma::cube&, arma::vec&, arma::vec&, const arma::mat&, arma::mat, const arma::cube&, arma::cube&, arma::mat&, arma::mat&, const arma::vec&)’:
mcmc_functions.cpp:1768:49: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
 1768 |         c_aik_1 = (arma::conv_to< double >::from( alpha_i_1.t()*bijectionvector(K) ));
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
mcmc_functions.cpp:1771:49: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
 1771 |         c_aik_0 = (arma::conv_to< double >::from( alpha_i_0.t()*bijectionvector(K) ));
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
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;
      |                                                             ^~~~~~
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++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native   -c resp_functions.cpp -o resp_functions.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rt_functions.cpp -o rt_functions.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native   -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++){
      |                           ~^~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:692,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
                 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:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/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;
      |                ^
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -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/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmpge1T6A/R.INSTALL391666596be522/hmcdm/src'
make[1]: Entering directory '/tmp/Rtmpge1T6A/R.INSTALL391666596be522/hmcdm/src'
make[1]: Leaving directory '/tmp/Rtmpge1T6A/R.INSTALL391666596be522/hmcdm/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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)