* installing *source* package ‘HDJM’ ...
** this is package ‘HDJM’ version ‘0.1.0’
** package ‘HDJM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/HDJM/src'
g++ -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/RcppEnsmallen/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 HDJM.cpp -o HDJM.o
HDJM.cpp: In function ‘arma::vec field_to_alpha_vec(const arma::field<arma::Col<double> >&, const arma::vec&, int, arma::uvec, arma::uvec)’:
HDJM.cpp:188:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  188 |     for(int j=0; j<idx.n_elem; j++){
      |                  ~^~~~~~~~~~~
HDJM.cpp: In function ‘arma::mat field_to_alpha_mat(const arma::field<arma::Mat<double> >&, const arma::vec&, int, const arma::uvec&, arma::uvec)’:
HDJM.cpp:206:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  206 |     for(int j=0; j<idx.n_elem; j++){
      |                  ~^~~~~~~~~~~
HDJM.cpp: In function ‘arma::field<arma::Col<double> > vec_to_field(const arma::vec&, const arma::uvec&)’:
HDJM.cpp:264:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  264 |     for(int k=0; k<p_z_vec.n_elem; k++){
      |                  ~^~~~~~~~~~~~~~~
HDJM.cpp: In function ‘arma::field<arma::Col<double> > vec_to_field_L(const arma::vec&, const arma::uvec&)’:
HDJM.cpp:279:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  279 |     for(int k=0; k<p_z_vec.n_elem; k++){
      |                  ~^~~~~~~~~~~~~~~
HDJM.cpp: In function ‘arma::vec field_to_vec(const arma::field<arma::Col<double> >&, const arma::uvec&)’:
HDJM.cpp:296:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  296 |     for(int k=0; k<p_z_vec.n_elem; k++){
      |                  ~^~~~~~~~~~~~~~~
HDJM.cpp: In function ‘arma::vec LowTriVec_field(const arma::field<arma::Mat<double> >&)’:
HDJM.cpp:309:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  309 |     for(int j =0; j< V.n_elem; j++){
      |                   ~^~~~~~~~~~
HDJM.cpp: In constructor ‘HDJM_para_t::HDJM_para_t(const Rcpp::List&)’:
HDJM.cpp:481:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  481 |         for(int k=0; k<beta.n_elem; k++){
      |                      ~^~~~~~~~~~~~
HDJM.cpp: In member function ‘void HDJM_para_t::NonZeroAlpha()’:
HDJM.cpp:496:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  496 |             for(int j=0; j<alpha_idx.n_elem; j++){
      |                          ~^~~~~~~~~~~~~~~~~
HDJM.cpp: In member function ‘void updateMuVFun::updateIntermediate()’:
HDJM.cpp:545:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  545 |         for(int j=0; j<para.alpha_idx.n_elem; j++){
      |                      ~^~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp: In member function ‘double updateMuVFun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
HDJM.cpp:572:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  572 |         for(int j=0; j< para.alpha_idx.n_elem;j++){
      |                      ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp:584:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  584 |         for(int jj=0;jj<h_it.n_elem; jj++){
      |                      ~~^~~~~~~~~~~~
HDJM.cpp:585:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  585 |             for(int j=0; j<para.alpha_idx.n_elem;j++){
      |                          ~^~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp:597:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  597 |         for(int j=0; j<para.alpha_idx.n_elem;j++){
      |                      ~^~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp:616:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  616 |         for(int j=0; j<para.alpha_idx.n_elem;j++){
      |                      ~^~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp:626:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  626 |         for(int j=0; j<para.alpha_idx.n_elem; j++){
      |                      ~^~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp: In function ‘arma::vec combineMuV(const HDJM_data_t&, const HDJM_para_t&, const int&)’:
HDJM.cpp:656:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  656 |     for(int j=0; j<para.alpha_idx.n_elem; j++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp: In function ‘void storeMuV(const HDJM_data_t&, HDJM_para_t&, const arma::vec&, const int&)’:
HDJM.cpp:683:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  683 |     for(int j=0; j< para.alpha_idx.n_elem;j++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp: In function ‘arma::vec combinePara(const HDJM_data_t&, const HDJM_para_t&)’:
HDJM.cpp:700:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  700 |     for(int j=0; j< para.alpha_idx.n_elem;j++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp: In function ‘void storePara(const arma::vec&, const HDJM_data_t&, HDJM_para_t&)’:
HDJM.cpp:729:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  729 |     for(int j=0; j< para.alpha_idx.n_elem;j++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp: In member function ‘double updateParaFun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
HDJM.cpp:775:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  775 |             for(int j=0; j< para.alpha_idx.n_elem;j++){
      |                          ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp:787:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  787 |                 for(int j=0; j< para.alpha_idx.n_elem;j++){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp:798:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  798 |             for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                          ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp:804:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  804 |             for(int jj=0; jj < h_it.n_elem; jj++){
      |                           ~~~^~~~~~~~~~~~~
HDJM.cpp:805:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  805 |                 for(int j=0; j<para.alpha_idx.n_elem; j++){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp:820:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  820 |             for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                          ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp: In function ‘double get_lammax(const HDJM_data_t&, const HDJM_para_t&, const arma::vec&)’:
HDJM.cpp:884:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  884 |             for(int jj=0; jj<tmp.n_elem; jj++){
      |                           ~~^~~~~~~~~~~
HDJM.cpp:903:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  903 |         for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                      ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp: In constructor ‘updateAlphaFun::updateAlphaFun(const HDJM_data_t&, const HDJM_para_t&, const arma::vec&)’:
HDJM.cpp:960:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  960 |                 for(int jj=0; jj<tmp.n_elem; jj++){
      |                               ~~^~~~~~~~~~~
HDJM.cpp: In member function ‘void updateAlphaFun::initiate()’:
HDJM.cpp:977:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  977 |                 for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp:983:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  983 |                     for(int jj=0; jj<tmp.n_elem; jj++){
      |                                   ~~^~~~~~~~~~~
HDJM.cpp:1004:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1004 |             for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                          ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp: In function ‘void updateSig(const HDJM_data_t&, HDJM_para_t&)’:
HDJM.cpp:1107:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1107 |         for(int j=0; j< para.alpha_idx.n_elem;j++){
      |                      ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp: In function ‘double calcELBO(const HDJM_data_t&, const HDJM_para_t&, const arma::mat&, const arma::vec&, double, double)’:
HDJM.cpp:1190:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1190 |     for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp:1201:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1201 |         for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                      ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp:1229:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1229 |             for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                          ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp:1240:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1240 |         for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                      ~^~~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp:1246:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1246 |         for(int jj=0; jj < h_it.n_elem; jj++){
      |                       ~~~^~~~~~~~~~~~~
HDJM.cpp:1247:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1247 |             for(int j=0; j<para.alpha_idx.n_elem; j++){
      |                          ~^~~~~~~~~~~~~~~~~~~~~~
HDJM.cpp: In function ‘Rcpp::List HDJM_seq(const Rcpp::List&, const Rcpp::List&, const arma::vec&, int, double, int, double, int, double, bool)’:
HDJM.cpp:1620:34: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
 1620 |         if(para.alpha_idx.n_elem > pmax){
      |            ~~~~~~~~~~~~~~~~~~~~~~^~~~~~
g++ -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/RcppEnsmallen/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++ -std=gnu++17 -shared -L/usr/local/lib64 -o HDJM.so HDJM.o RcppExports.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/HDJM/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/HDJM/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/HDJM/src'
installing to /data/gannet/ripley/R/packages/tests-devel/HDJM.Rcheck/00LOCK-HDJM/00new/HDJM/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (HDJM)