* installing *source* package ‘HDJM’ ...
** package ‘HDJM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.0.1 20240430 (prerelease)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/HDJM/src'
g++-14 -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++-14 -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++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -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)