* installing *source* package ‘sommer’ ...
** package ‘sommer’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/sommer/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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fopenmp -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 -DR_NO_REMAP -c MNR.cpp -o MNR.o
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/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fopenmp -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 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
MNR.cpp: In function 'arma::mat dmat(const arma::mat&, const bool&, double)':
MNR.cpp:306:7: warning: unused variable 'p' [-Wunused-variable]
306 | int p = X.n_cols;
| ^
MNR.cpp: In function 'arma::rowvec scorecalc(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, int, double)':
MNR.cpp:453:23: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
453 | for (int i = 0; i < b.n_rows; ++i) {
| ~~^~~~~~~~~~
MNR.cpp: In function 'Rcpp::List MNR(const arma::mat&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const bool&, int, double, double, const bool&, const bool&, const bool&, const bool&, const arma::vec&, const arma::vec&)':
MNR.cpp:635:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
635 | for(int h=0; h < provX.n_cols ; h++){ // for each random effect unlist
| ~~^~~~~~~~~~~~~~
MNR.cpp: In function 'Rcpp::List ai_mme_sp(const arma::sp_mat&, const Rcpp::List&, const arma::vec&, const Rcpp::List&, const arma::sp_mat&, const Rcpp::List&, const Rcpp::List&, const arma::sp_mat&, const bool&, int, double, double, double, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const arma::vec&, const arma::vec&, const arma::vec&, const bool&)':
MNR.cpp:1299:12: warning: unused variable 'ok' [-Wunused-variable]
1299 | bool ok = log_det(val, sign, arma::mat(Ai[i])); // calculate the logDet of the covariance matrix
| ^~
MNR.cpp:1522:14: warning: unused variable 'ok' [-Wunused-variable]
1522 | bool ok = log_det(val, sign, theta(i)); // form 2
| ^~
MNR.cpp:1570:32: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
1570 | for(int iRow = 0; iRow < partitionsP.n_rows; ++iRow){ // for each partition row
| ~~~~~^~~~~~~~~~~~~~~~~~~~
MNR.cpp:1588:32: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
1588 | for(int iRow = 0; iRow < lambdaProv.n_rows; ++iRow){
| ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1589:34: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
1589 | for(int iCol = 0; iCol < lambdaProv.n_cols; ++iCol){
| ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1614:24: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'unsigned int'} [-Wsign-compare]
1614 | for(int iS = 0; iS < S.size(); ++iS){
| ~~~^~~~~~~~~~
MNR.cpp:1695:32: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
1695 | for(int iRow = 0; iRow < lambdaProv.n_rows; ++iRow){
| ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1696:34: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
1696 | for(int iCol = 0; iCol < lambdaProv.n_cols; ++iCol){
| ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1722:24: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'unsigned int'} [-Wsign-compare]
1722 | for(int iS = 0; iS < S.size(); ++iS){ // Rij <- S[[iS]]%*%Ri
| ~~~^~~~~~~~~~
MNR.cpp:1780:22: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'unsigned int'} [-Wsign-compare]
1780 | for(int i = 0; i < thetaCUnlisted.size() ; ++i){
| ~~^~~~~~~~~~~~~~~~~~~~~~~
MNR.cpp:1787:28: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
1787 | for(int j = 0; j < toBoundary.n_cols ; ++j){
| ~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1528:10: warning: unused variable 'ok' [-Wunused-variable]
1528 | bool ok = log_det(val, sign, theta(nRRe-1)); // form 2
| ^~
MNR.cpp: In function 'arma::vec varCols(const arma::mat&)':
MNR.cpp:148:19: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized]
148 | out(j) = M2/(n-1);
| ~~^~~
MNR.cpp:138:9: note: 'n' was declared here
138 | int n;
| ^
MNR.cpp: In function 'Rcpp::List MNR(const arma::mat&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const bool&, int, double, double, const bool&, const bool&, const bool&, const bool&, const arma::vec&, const arma::vec&)':
MNR.cpp:1108:36: warning: 'cycle2' may be used uninitialized [-Wmaybe-uninitialized]
1108 | arma::mat monitor2 = monitor.cols(0, cycle2);
| ~~~~~~~~~~~~^~~~~~~~~~~
MNR.cpp:719:14: note: 'cycle2' was declared here
719 | int cycle, cycle2, ikk;
| ^~~~~~
MNR.cpp:1099:20: warning: 'llik' may be used uninitialized [-Wmaybe-uninitialized]
1099 | double AIC = (-2 * llik) + (2 * Xm.n_cols);
| ~~~~^~~~~~~
MNR.cpp:720:16: note: 'llik' was declared here
720 | double ldet, llik, llik0, delta_llik, checkP, seconds; // to store likelihoods and determinants
| ^~~~
MNR.cpp: In function 'Rcpp::List ai_mme_sp(const arma::sp_mat&, const Rcpp::List&, const arma::vec&, const Rcpp::List&, const arma::sp_mat&, const Rcpp::List&, const Rcpp::List&, const arma::sp_mat&, const bool&, int, double, double, double, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const arma::vec&, const arma::vec&, const arma::vec&, const bool&)':
MNR.cpp:1286:37: warning: 'nRe' may be used uninitialized [-Wmaybe-uninitialized]
1286 | arma::field<arma::sp_mat> Ai(nReAl); // allocate size of Ai field
| ^
MNR.cpp:1245:7: note: 'nRe' was declared here
1245 | int nRe;
| ^~~
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o sommer.so MNR.o RcppExports.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/sommer/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/sommer/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/sommer/src'
installing to /data/gannet/ripley/R/packages/tests-devel/sommer.Rcheck/00LOCK-sommer/00new/sommer/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (sommer)