* installing *source* package ‘PJFM’ ...
** this is package ‘PJFM’ version ‘0.1.0’
** package ‘PJFM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/PJFM/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 PJFMcovBD.cpp -o PJFMcovBD.o
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
PJFMcovBD.cpp: In function ‘arma::vec field_to_alpha_vec(const arma::field<arma::Col<double> >&, const arma::vec&, int, arma::uvec, arma::uvec)’:
PJFMcovBD.cpp:108:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  108 |   for(int j=0; j<idx.n_elem; j++){
      |                ~^~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::vec field_to_alpha_vec_full(const arma::field<arma::Col<double> >&, const arma::vec&, int, arma::uvec)’:
PJFMcovBD.cpp:126:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  126 |   for(int k=0; k<alpha.n_elem; k++){
      |                ~^~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::mat field_to_alpha_mat(const arma::field<arma::Mat<double> >&, const arma::vec&, int, const arma::uvec&, arma::uvec)’:
PJFMcovBD.cpp:144:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  144 |   for(int j=0; j<idx.n_elem; j++){
      |                ~^~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::mat field_to_alpha_mat_full(const arma::field<arma::Mat<double> >&, const arma::vec&, int, const arma::uvec&)’:
PJFMcovBD.cpp:162:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  162 |   for(int k=0; k<alpha.n_elem; k++){
      |                ~^~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::mat field_to_zero_mat_full(const arma::field<arma::Mat<double> >&, const arma::vec&, int, const arma::uvec&, int)’:
PJFMcovBD.cpp:179:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  179 |   for(int k=0; k<alpha.n_elem; k++){
      |                ~^~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::mat field_to_zero_noalpha_mat_full(const arma::field<arma::Mat<double> >&, int, const arma::uvec&, int)’:
PJFMcovBD.cpp:199:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  199 |   for(int k=0; k < p_x_vec.n_elem; k++){
      |                ~~^~~~~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::field<arma::Col<double> > vec_to_field(const arma::vec&, const arma::uvec&)’:
PJFMcovBD.cpp:258:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  258 |   for(int k=0; k<p_z_vec.n_elem; k++){
      |                ~^~~~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::field<arma::Col<double> > vec_to_field_L(const arma::vec&, const arma::uvec&)’:
PJFMcovBD.cpp:273:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  273 |   for(int k=0; k<p_z_vec.n_elem; k++){
      |                ~^~~~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::vec field_to_vec(const arma::field<arma::Col<double> >&, const arma::uvec&)’:
PJFMcovBD.cpp:289:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  289 |   for(int k=0; k<p_z_vec.n_elem; k++){
      |                ~^~~~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::vec LowTriVec_field(const arma::field<arma::Mat<double> >&)’:
PJFMcovBD.cpp:302:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  302 |   for(int j =0; j< V.n_elem; j++){
      |                 ~^~~~~~~~~~
PJFMcovBD.cpp: In function ‘double CoxFM_calcELBO(const CoxFM_data_t&, const CoxFM_para_t&)’:
PJFMcovBD.cpp:418:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  418 |     for(int j=0; j< h_it.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp: In member function ‘double CoxFM_updateBetaFun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
PJFMcovBD.cpp:484:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  484 |       for(int j=0; j< h_it.n_elem; j++){
      |                    ~^~~~~~~~~~~~~
PJFMcovBD.cpp: In member function ‘double CoxFM_updateMuVFun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
PJFMcovBD.cpp:537:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  537 |     for(int j=0; j< h_it.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp: In member function ‘void PJFM_para_t::MakeDiagonal()’:
PJFMcovBD.cpp:916:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  916 |     for(int i=0; i<V.n_elem; i++){
      |                  ~^~~~~~~~~
PJFMcovBD.cpp: In function ‘double PJFM_calcELBO(const PJFM_data_t&, const PJFM_para_t&)’:
PJFMcovBD.cpp:957:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  957 |       for(int j=0; j< h_it.n_elem; j++){
      |                    ~^~~~~~~~~~~~~
PJFMcovBD.cpp:987:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  987 |     for(int j=0; j< h_it.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp: In member function ‘double PJFM_updateAlphaFun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
PJFMcovBD.cpp:1052:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1052 |       for(int j=0; j< h_it.n_elem; j++){
      |                    ~^~~~~~~~~~~~~
PJFMcovBD.cpp:1065:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1065 |       for(int k=0; k < alpha.n_elem;k++){
      |                    ~~^~~~~~~~~~~~~~
PJFMcovBD.cpp:1072:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1072 |         for(int j=0; j< XBZmu.n_elem; j++){
      |                      ~^~~~~~~~~~~~~~
PJFMcovBD.cpp: In member function ‘double PJFM_updateAlpha_lasso_Fun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
PJFMcovBD.cpp:1136:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1136 |       for(int j=0; j< h_it.n_elem; j++){
      |                    ~^~~~~~~~~~~~~
PJFMcovBD.cpp:1149:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1149 |       for(int k=0; k < alpha.n_elem;k++){
      |                    ~~^~~~~~~~~~~~~~
PJFMcovBD.cpp:1156:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1156 |         for(int j=0; j< XBZmu.n_elem; j++){
      |                      ~^~~~~~~~~~~~~~
PJFMcovBD.cpp: In member function ‘double PJFM_updateBetaALLFun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
PJFMcovBD.cpp:1221:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1221 |         for(int j=0; j< h_it.n_elem; j++){
      |                      ~^~~~~~~~~~~~~
PJFMcovBD.cpp:1249:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1249 |       for(int j=0; j< h_it.n_elem; j++){
      |                    ~^~~~~~~~~~~~~
PJFMcovBD.cpp: In member function ‘double PJFM_updateMuVFun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
PJFMcovBD.cpp:1321:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1321 |       for(int j=0; j< h_it.n_elem; j++){
      |                    ~^~~~~~~~~~~~~
PJFMcovBD.cpp:1364:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1364 |     for(int j=0; j< h_it.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp: In member function ‘double PJFM_updateMuVFun_Diag::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
PJFMcovBD.cpp:1471:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1471 |       for(int j=0; j< h_it.n_elem; j++){
      |                    ~^~~~~~~~~~~~~
PJFMcovBD.cpp:1515:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1515 |     for(int j=0; j< h_it.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::mat calcHessian(const PJFM_data_t&, const PJFM_para_t&)’:
PJFMcovBD.cpp:1696:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1696 |   for(int j=0; j<p_all_vec.n_elem;j++){
      |                ~^~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:1735:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1735 |       for(int j=0; j< h_it_recur.n_rows; j++){
      |                    ~^~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:1755:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1755 |     for(int j=0; j< h_it.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp:1809:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1809 |       for(int j=0; j<h_it.n_elem; j++){
      |                    ~^~~~~~~~~~~~
PJFMcovBD.cpp:1835:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1835 |     for(int j=0; j< Z_iD.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp:1862:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1862 |     for(int j=0; j< Z_iD.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp:1872:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1872 |     for(int j=0; j< Z_iD.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp:1902:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1902 |     for(int j=0; j<h_it.n_elem; j++){
      |                  ~^~~~~~~~~~~~
PJFMcovBD.cpp:1909:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1909 |     for(int j=0; j<h_it.n_elem; j++){
      |                  ~^~~~~~~~~~~~
PJFMcovBD.cpp:1956:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1956 |       for(int j=0; j<h_it.n_elem; j++){
      |                    ~^~~~~~~~~~~~
PJFMcovBD.cpp:1969:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1969 |     for(int j=0; j< h_it.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::mat calcHessianSUB(const PJFM_data_t&, const PJFM_para_t&)’:
PJFMcovBD.cpp:2032:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2032 |   for(int j=0; j<p_all_vec.n_elem;j++){
      |                ~^~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:2071:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2071 |       for(int j=0; j< h_it_recur.n_rows; j++){
      |                    ~^~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:2091:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2091 |     for(int j=0; j< h_it.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp:2145:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2145 |       for(int j=0; j<h_it.n_elem; j++){
      |                    ~^~~~~~~~~~~~
PJFMcovBD.cpp:2171:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2171 |     for(int j=0; j< Z_iD.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp:2198:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2198 |     for(int j=0; j< Z_iD.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp:2208:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2208 |     for(int j=0; j< Z_iD.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp:2238:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2238 |     for(int j=0; j<h_it.n_elem; j++){
      |                  ~^~~~~~~~~~~~
PJFMcovBD.cpp:2245:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2245 |     for(int j=0; j<h_it.n_elem; j++){
      |                  ~^~~~~~~~~~~~
PJFMcovBD.cpp:2292:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2292 |       for(int j=0; j<h_it.n_elem; j++){
      |                    ~^~~~~~~~~~~~
PJFMcovBD.cpp:2305:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2305 |     for(int j=0; j< h_it.n_elem; j++){
      |                  ~^~~~~~~~~~~~~
PJFMcovBD.cpp: In constructor ‘PJFM_para_covBD_t::PJFM_para_covBD_t(const Rcpp::List&)’:
PJFMcovBD.cpp:2959:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2959 |     for(int k=0; k<beta.n_elem; k++){
      |                  ~^~~~~~~~~~~~
PJFMcovBD.cpp: In member function ‘void PJFM_para_covBD_t::NonZeroAlpha()’:
PJFMcovBD.cpp:2973:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2973 |       for(int j=0; j<alpha_idx.n_elem; j++){
      |                    ~^~~~~~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::mat PJFM_calcELBO_baseRecur(const PJFM_data_t&, const PJFM_para_covBD_t&)’:
PJFMcovBD.cpp:3006:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3006 |       for(int j=0; j< h_it.n_elem; j++){
      |                    ~^~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘double PJFM_calcELBO_covBD(const PJFM_data_t&, const PJFM_para_covBD_t&, const arma::mat&, const arma::vec&, double, double)’:
PJFMcovBD.cpp:3052:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3052 |   for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3060:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3060 |     for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3068:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3068 |       for(int j=0; j< h_it.n_elem; j++){
      |                    ~^~~~~~~~~~~~~
PJFMcovBD.cpp:3094:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3094 |       for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                    ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3102:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3102 |     for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3107:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3107 |     for(int jj=0; jj < h_it.n_elem; jj++){
      |                   ~~~^~~~~~~~~~~~~
PJFMcovBD.cpp:3108:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3108 |       for(int j=0; j<para.alpha_idx.n_elem; j++){
      |                    ~^~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘double PJFM_get_lammax_covBD(const PJFM_data_t&, const PJFM_para_covBD_t&, const arma::vec&)’:
PJFMcovBD.cpp:3149:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3149 |       for(int jj=0; jj<tmp.n_elem; jj++){
      |                     ~~^~~~~~~~~~~
PJFMcovBD.cpp:3164:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3164 |     for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp: In member function ‘double PJFM_updateAlphaVecLasso_covBD_Fun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
PJFMcovBD.cpp:3222:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3222 |         for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                      ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3244:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3244 |       for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                    ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3249:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3249 |       for(int jj=0; jj < h_it.n_elem; jj++){
      |                     ~~~^~~~~~~~~~~~~
PJFMcovBD.cpp:3250:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3250 |         for(int j=0; j<para.alpha_idx.n_elem; j++){
      |                      ~^~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3266:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3266 |       for(int j=0; j < alpha.n_elem;j++){
      |                    ~~^~~~~~~~~~~~~~
PJFMcovBD.cpp:3273:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3273 |         for(int jj=0; jj< XBZmu.n_elem; jj++){
      |                       ~~^~~~~~~~~~~~~~
PJFMcovBD.cpp: In constructor ‘PJFM_updateAlphaLasso_covBD_Fun::PJFM_updateAlphaLasso_covBD_Fun(const PJFM_data_t&, const PJFM_para_covBD_t&, const arma::vec&)’:
PJFMcovBD.cpp:3335:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3335 |         for(int jj=0; jj<tmp.n_elem; jj++){
      |                       ~~^~~~~~~~~~~
PJFMcovBD.cpp: In member function ‘void PJFM_updateAlphaLasso_covBD_Fun::initiate()’:
PJFMcovBD.cpp:3352:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3352 |         for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                      ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3356:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3356 |           for(int jj=0; jj<tmp.n_elem; jj++){
      |                         ~~^~~~~~~~~~~
PJFMcovBD.cpp:3372:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3372 |       for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                    ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::vec PJFM_combineBeta_covBD(const PJFM_data_t&, const PJFM_para_covBD_t&)’:
PJFMcovBD.cpp:3479:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3479 |   for(int j=0; j< para.alpha_idx.n_elem;j++){
      |                ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘void PJFM_storeBeta_covBD(arma::vec, const PJFM_data_t&, PJFM_para_covBD_t&)’:
PJFMcovBD.cpp:3499:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3499 |   for(int j=0; j< para.alpha_idx.n_elem;j++){
      |                ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp: In member function ‘double PJFM_updateBetaALL_covBD_Fun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
PJFMcovBD.cpp:3528:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3528 |     for(int k=0; k < para.alpha_idx.n_elem; k++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3538:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3538 |       for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                    ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3545:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3545 |         for(int j=0; j< h_it.n_elem; j++){
      |                      ~^~~~~~~~~~~~~
PJFMcovBD.cpp:3567:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3567 |       for(int j=0; j< para.alpha_idx.n_elem; j++){
      |                    ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3572:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3572 |       for(int jj=0; jj < h_it.n_elem; jj++){
      |                     ~~~^~~~~~~~~~~~~
PJFMcovBD.cpp:3573:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3573 |         for(int j=0; j<para.alpha_idx.n_elem; j++){
      |                      ~^~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘arma::vec PJFM_combineMuV_covBD(const PJFM_data_t&, const PJFM_para_covBD_t&, const int&)’:
PJFMcovBD.cpp:3672:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3672 |   for(int j=0; j<para.alpha_idx.n_elem; j++){
      |                ~^~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘void PJFM_storeMuV_covBD(const PJFM_data_t&, PJFM_para_covBD_t&, const arma::vec&, const int&)’:
PJFMcovBD.cpp:3699:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3699 |   for(int j=0; j< para.alpha_idx.n_elem;j++){
      |                ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp: In member function ‘double PJFM_updateMuV_covBD_Fun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
PJFMcovBD.cpp:3747:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3747 |     for(int j=0; j< para.alpha_idx.n_elem;j++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3769:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3769 |     for(int j =0; j<para.alpha_idx.n_elem;j++){
      |                   ~^~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3779:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3779 |       for(int jj=0; jj< h_it.n_elem; jj++){
      |                     ~~^~~~~~~~~~~~~
PJFMcovBD.cpp:3806:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3806 |       for(int j =0; j<para.alpha_idx.n_elem;j++){
      |                     ~^~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3815:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3815 |     for(int jj=0;jj<h_it.n_elem; jj++){
      |                  ~~^~~~~~~~~~~~
PJFMcovBD.cpp:3816:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3816 |       for(int j=0; j<para.alpha_idx.n_elem;j++){
      |                    ~^~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3832:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3832 |     for(int j=0; j<para.alpha_idx.n_elem;j++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3842:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3842 |     for(int j=0; j<para.alpha_idx.n_elem;j++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3850:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3850 |     for(int j=0; j<para.alpha_idx.n_elem; j++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘void PJFM_updateSig_covBD(const PJFM_data_t&, PJFM_para_covBD_t&)’:
PJFMcovBD.cpp:3883:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3883 |     for(int j=0; j< para.alpha_idx.n_elem;j++){
      |                  ~^~~~~~~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘bool check_para(const PJFM_para_covBD_t&)’:
PJFMcovBD.cpp:3921:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3921 |   for(int k=0; k<para.Sigma.n_elem; k++){
      |                ~^~~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3928:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3928 |   for(int k=0; k<para.beta.n_elem; k++){
      |                ~^~~~~~~~~~~~~~~~~
PJFMcovBD.cpp:3935:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3935 |   for(int i=0; i<para.mu.n_rows; i++ ){
      |                ~^~~~~~~~~~~~~~~
PJFMcovBD.cpp:3936:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3936 |     for(int k=0; k <para.mu.n_cols; k++ ){
      |                  ~~^~~~~~~~~~~~~~~
PJFMcovBD.cpp:3945:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3945 |   for(int i=0; i<para.V.n_rows; i++ ){
      |                ~^~~~~~~~~~~~~~
PJFMcovBD.cpp:3946:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3946 |     for(int k=0; k <para.V.n_cols; k++ ){
      |                  ~~^~~~~~~~~~~~~~
PJFMcovBD.cpp: In function ‘Rcpp::List PJFM_covBD_seq(const Rcpp::List&, const Rcpp::List&, const arma::vec&, int, double, int, double, int, double, bool)’:
PJFMcovBD.cpp:4293:30: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
 4293 |     if(para.alpha_idx.n_elem > pmax){
      |        ~~~~~~~~~~~~~~~~~~~~~~^~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o PJFM.so PJFMcovBD.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/PJFM/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/PJFM/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/PJFM/src'
installing to /data/gannet/ripley/R/packages/tests-devel/PJFM.Rcheck/00LOCK-PJFM/00new/PJFM/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 (PJFM)