* installing *source* package ‘sommer’ ...
** this is package ‘sommer’ version ‘4.4.87’
** package ‘sommer’ successfully unpacked and MD5 sums checked
** using staged installation
configure: METIS not found - using Eigen's built-in AMD ordering (default).
** libs
using C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/sommer/src'
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppProgress/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -I/usr/local/include -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 -c MNR.cpp -o MNR.o
MNR.cpp: In function ‘arma::cube scorecalc(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, int, double)’:
MNR.cpp:498:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
498 | for (int i = 0; i < b.n_rows; ++i) {
| ~~^~~~~~~~~~
MNR.cpp: In function ‘Rcpp::List newton_di_sp(const arma::sp_mat&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::sp_mat&, const bool&, int, double, double, const bool&, const bool&, const bool&, const bool&, const arma::vec&, const arma::vec&, const Rcpp::List&, const arma::vec&)’:
MNR.cpp:686:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
686 | for(int h=0; h < provX.n_cols ; h++){ // for each random effect unlist
| ~~^~~~~~~~~~~~~~
MNR.cpp:1184:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
1184 | for (int j = 0; j < thetaConstOriIth.n_cols; ++j) { // for each row in theta
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~
MNR.cpp:1185:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
1185 | for (int k = 0; k < thetaConstOriIth.n_rows; ++k) { // for each col in theta
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~
MNR.cpp:1198:36: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
1198 | if( blupTable.n_cols <= j){ // not yet populated
| ~~~~~~~~~~~~~~~~~^~~~
MNR.cpp:1230:35: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
1230 | if(blupTable.n_cols <= j){ // not yet populated
| ~~~~~~~~~~~~~~~~~^~~~
MNR.cpp:1241:36: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
1241 | if( blupTable.n_cols <= k){ // not yet populated
| ~~~~~~~~~~~~~~~~~^~~~
MNR.cpp:1266:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
1266 | for (int l = 0; l < blupTable.n_cols; ++l) {
| ~~^~~~~~~~~~~~~~~~~~
MNR.cpp:1287:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
1287 | for (int i = 0; i < partitions.size(); ++i) {//for each major random effect
| ~~^~~~~~~~~~~~~~~~~~~
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:2377:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
2377 | for(int iRow = 0; iRow < partitionsP.n_rows; ++iRow){ // for each partition row
| ~~~~~^~~~~~~~~~~~~~~~~~~~
MNR.cpp:2394:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
2394 | for(int iRow = 0; iRow < lambda(iR).n_rows; ++iRow){
| ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:2395:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
2395 | for(int iCol = 0; iCol < lambda(iR).n_cols; ++iCol){
| ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:2418:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
2418 | for(int iS = 0; iS < Si.size(); ++iS){
| ~~~^~~~~~~~~~~
MNR.cpp:2479:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
2479 | for(int iRow = 0; iRow < lambda(iR).n_rows; ++iRow){
| ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:2480:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
2480 | for(int iCol = 0; iCol < lambda(iR).n_cols; ++iCol){
| ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:2506:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
2506 | for(int iS = 0; iS < Si.size(); ++iS){ // Rij <- S[[iS]]%*%Ri
| ~~~^~~~~~~~~~~
MNR.cpp:2550:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
2550 | for(int i = 0; i < thetaCUnlisted.size() ; ++i){
| ~~^~~~~~~~~~~~~~~~~~~~~~~
MNR.cpp:2557:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
2557 | for(int j = 0; j < toBoundary.n_cols ; ++j){
| ~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:2733:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
2733 | for (int j = 0; j < partitionsP.n_rows; ++j) {
| ~~^~~~~~~~~~~~~~~~~~~~
MNR.cpp:2001:10: warning: unused variable ‘vary2’ [-Wunused-variable]
2001 | double vary2 = arma::mean(arma::var(arma::square(y0)));
| ^~~~~
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:2891:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
2891 | for(int h=0; h < provX.n_cols ; h++){ // for each random effect unlist
| ~~^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppProgress/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -I/usr/local/include -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 -c RcppExports.cpp -o RcppExports.o
MNR.cpp: In function ‘Rcpp::List ai_mme_sp2(const arma::sp_mat&, const Rcpp::List&, const arma::vec&, const Rcpp::List&, const arma::sp_mat&, const arma::sp_mat&, const bool&, const arma::uvec&, const arma::uvec&, int, double, double, double, const Rcpp::List&, const arma::vec&, const arma::vec&, const bool&, const int&, const std::string&, const double&, const int&, const int&, const int&, const bool&, const bool&, const double&, const double&, const bool&)’:
MNR.cpp:12811:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
12811 | for(int j = 0; j < toBoundary.n_cols; ++j){
| ~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:14245:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
14245 | for (int j = 0; j < partitionsP.n_rows; ++j) {
| ~~^~~~~~~~~~~~~~~~~~~~
MNR.cpp: In function ‘arma::vec varCols(const arma::mat&)’:
MNR.cpp:192:19: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized]
192 | out(j) = M2/(n-1);
| ~~^~~
MNR.cpp:182:9: note: ‘n’ was declared here
182 | 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:3348:36: warning: ‘cycle2’ may be used uninitialized [-Wmaybe-uninitialized]
3348 | arma::mat monitor2 = monitor.cols(0, cycle2);
| ~~~~~~~~~~~~^~~~~~~~~~~
MNR.cpp:2969:14: note: ‘cycle2’ was declared here
2969 | int cycle, cycle2, ikk;
| ^~~~~~
MNR.cpp:3339:20: warning: ‘llik’ may be used uninitialized [-Wmaybe-uninitialized]
3339 | double AIC = (-2 * llik) + (2 * Xm.n_cols);
| ~~~~^~~~~~~
MNR.cpp:2970:16: note: ‘llik’ was declared here
2970 | double ldet, llik, llik0, delta_llik, checkP, seconds; // to store likelihoods and determinants
| ^~~~
MNR.cpp: In function ‘Rcpp::List newton_di_sp(const arma::sp_mat&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::sp_mat&, const bool&, int, double, double, const bool&, const bool&, const bool&, const bool&, const arma::vec&, const arma::vec&, const Rcpp::List&, const arma::vec&)’:
MNR.cpp:1164:48: warning: ‘cycle2’ may be used uninitialized [-Wmaybe-uninitialized]
1164 | sigma_perc_change2 = sigma_perc_change.cols(1, cycle2); // indicate first and last column to subset to return at the end
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
MNR.cpp:771:14: note: ‘cycle2’ was declared here
771 | int cycle, cycle2, ikk;
| ^~~~~~
MNR.cpp:1152:20: warning: ‘llik’ may be used uninitialized [-Wmaybe-uninitialized]
1152 | double AIC = (-2 * llik) + (2 * Xm.n_cols);
| ~~~~^~~~~~~
MNR.cpp:772:16: note: ‘llik’ was declared here
772 | double ldet, llik, llik0, delta_llik, checkP, seconds; // to store likelihoods and determinants
| ^~~~
In file included from /data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/Core:337,
from /data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/SparseCore:11,
from MNR.cpp:12:
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function ‘static void Eigen::internal::selfadjoint_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, false>; Lhs = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; int LhsMode = 17; Rhs = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, -1, 1> >, const Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true>, -1, 1, false> >]’:
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized]
227 | internal::selfadjoint_matrix_vector_product<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::Flags&RowMajorBit) ? RowMajor : ColMajor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | (
| ^
230 | lhs.rows(), // size
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
232 | actualRhsPtr, // rhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
233 | actualDestPtr, // result info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
234 | actualAlpha // scale factor
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
235 | );
| ~
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type ‘const double*’ to ‘static void Eigen::internal::selfadjoint_matrix_vector_product<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]’ declared here
41 | void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::run(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/Core:341:
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘static void Eigen::internal::trmv_selector<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 1, -1, true>, 1, -1, false> >; int Mode = 6]’:
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized]
327 | internal::triangular_matrix_vector_product
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | <Index,Mode,
| ~~~~~~~~~~~~
329 | LhsScalar, LhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
330 | RhsScalar, RhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
331 | RowMajor>
| ~~~~~~~~~
332 | ::run(actualLhs.rows(),actualLhs.cols(),
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
333 | actualLhs.data(),actualLhs.outerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
334 | actualRhsPtr,1,
| ~~~~~~~~~~~~~~~
335 | dest.data(),dest.innerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
336 | actualAlpha);
| ~~~~~~~~~~~~
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here
105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -shared -L/usr/local/lib64 -o sommer.so MNR.o RcppExports.o -fopenmp -llapack -L/data/localhost/ripley/R/R-devel/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/sommer/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/sommer/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/sommer/src'
installing to /data/localhost/ripley/R/packages/tests-devel/sommer.Rcheck/00LOCK-sommer/00new/sommer/libs
** R
** 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)