* installing *source* package ‘VBJM’ ...
** this is package ‘VBJM’ version ‘0.1.0’
** package ‘VBJM’ 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/VBJM/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 RcppExports.cpp -o RcppExports.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 VBJM.cpp -o VBJM.o
VBJM.cpp: In function ‘arma::vec field_to_alpha_vec(const arma::field<arma::Col<double> >&, const arma::vec&, int, arma::uvec)’:
VBJM.cpp:210:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  210 |     for(int k=0; k<alpha.n_elem; k++){
      |                  ~^~~~~~~~~~~~~
VBJM.cpp: In function ‘arma::mat field_to_alpha_mat(const arma::field<arma::Mat<double> >&, const arma::vec&, int, const arma::uvec&)’:
VBJM.cpp:226:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  226 |     for(int k=0; k<alpha.n_elem; k++){
      |                  ~^~~~~~~~~~~~~
VBJM.cpp: In function ‘arma::field<arma::Col<double> > vec_to_field(const arma::vec&, const arma::uvec&)’:
VBJM.cpp:283:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  283 |     for(int k=0; k<p_z_vec.n_elem; k++){
      |                  ~^~~~~~~~~~~~~~~
VBJM.cpp: In function ‘arma::vec field_to_vec(const arma::field<arma::Col<double> >&, const arma::uvec&)’:
VBJM.cpp:300:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  300 |     for(int k=0; k<p_z_vec.n_elem; k++){
      |                  ~^~~~~~~~~~~~~~~
VBJM.cpp: In constructor ‘VBJM_para_t::VBJM_para_t(const Rcpp::List&)’:
VBJM.cpp:450:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  450 |         for(int k=0; k<beta.n_elem; k++){
      |                      ~^~~~~~~~~~~~
VBJM.cpp: In member function ‘double updateMuVFun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
VBJM.cpp:538:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  538 |         for(int j=0;j<h_it.n_elem; j++){
      |                     ~^~~~~~~~~~~~
VBJM.cpp:551:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  551 |         for(int k=0; k< Ytmp.n_elem; k++){
      |                      ~^~~~~~~~~~~~~
VBJM.cpp:569:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  569 |         for(int k=0; k<data.p_z_vec.n_elem; k++){
      |                      ~^~~~~~~~~~~~~~~~~~~~
VBJM.cpp: In member function ‘double updateMuFun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
VBJM.cpp:693:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  693 |         for(int k=0; k< Ytmp.n_elem; k++){
      |                      ~^~~~~~~~~~~~~
VBJM.cpp:711:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  711 |         for(int k=0; k<data.p_z_vec.n_elem; k++){
      |                      ~^~~~~~~~~~~~~~~~~~~~
VBJM.cpp: In member function ‘double updateParaFun::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
VBJM.cpp:991:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  991 |             for(int j=0; j< h_it.n_elem; j++){
      |                          ~^~~~~~~~~~~~~
VBJM.cpp:1032:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1032 |             for(int k=0; k < alpha.n_elem;k++){
      |                          ~~^~~~~~~~~~~~~~
VBJM.cpp:1041:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1041 |                 for(int j=0; j< XBZmu.n_elem; j++){
      |                              ~^~~~~~~~~~~~~~
VBJM.cpp: In member function ‘double updateParaFunLP::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
VBJM.cpp:1235:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1235 |             for(int k=0; k < alpha.n_elem;k++){
      |                          ~~^~~~~~~~~~~~~~
VBJM.cpp:1256:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1256 |                 for(int j=0; j< XBZmu.n_elem; j++){
      |                              ~^~~~~~~~~~~~~~
VBJM.cpp: In member function ‘double updateParaFunQPL::EvaluateWithGradient(const arma::mat&, arma::mat&)’:
VBJM.cpp:1457:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1457 |             for(int k=0; k < alpha.n_elem;k++){
      |                          ~~^~~~~~~~~~~~~~
VBJM.cpp: In function ‘double calcELBO(const VBJM_data_t&, const VBJM_para_t&)’:
VBJM.cpp:1584:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1584 |         for(int j=0; j< h_it.n_elem; j++){
      |                      ~^~~~~~~~~~~~~
VBJM.cpp: In function ‘arma::mat calcHessian(const VBJM_data_t&, const VBJM_para_t&)’:
VBJM.cpp:1868:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1868 |     for(int j=0; j<p_all_vec.n_elem;j++){
      |                  ~^~~~~~~~~~~~~~~~~
VBJM.cpp:1915:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1915 |         for(int j=0; j< h_it.n_elem; j++){
      |                      ~^~~~~~~~~~~~~
VBJM.cpp:1940:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1940 |         for(int j=0; j<h_it.n_elem; j++){
      |                      ~^~~~~~~~~~~~
VBJM.cpp:1981:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1981 |             for(int j=0; j<D1h_alpha(k).n_elem; j++){
      |                          ~^~~~~~~~~~~~~~~~~~~~
VBJM.cpp:2051:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2051 |         for(int j=0; j<h_it.n_elem; j++){
      |                      ~^~~~~~~~~~~~
VBJM.cpp:2058:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2058 |         for(int j=0; j<h_it.n_elem; j++){
      |                      ~^~~~~~~~~~~~
VBJM.cpp:2107:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2107 |         for(int j=0; j<h_it.n_elem; j++){
      |                      ~^~~~~~~~~~~~
VBJM.cpp:2114:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2114 |         for(int j=0; j<h_it.n_elem; j++){
      |                      ~^~~~~~~~~~~~
VBJM.cpp:2136:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2136 |         for(int j=0; j< X_iD.n_elem; j++){
      |                      ~^~~~~~~~~~~~~
VBJM.cpp:2171:23: 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< X_iD.n_elem; j++){
      |                      ~^~~~~~~~~~~~~
VBJM.cpp:2181:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2181 |         for(int j=0; j< X_iD.n_elem; j++){
      |                      ~^~~~~~~~~~~~~
VBJM.cpp:2238:23: 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< e_it.n_elem; j++){
      |                      ~^~~~~~~~~~~~~
VBJM.cpp:2325:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2325 |         for(int j=0; j< h_it.n_elem; j++){
      |                      ~^~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o VBJM.so RcppExports.o VBJM.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/VBJM/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/VBJM/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/VBJM/src'
installing to /data/gannet/ripley/R/packages/tests-devel/VBJM.Rcheck/00LOCK-VBJM/00new/VBJM/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 (VBJM)