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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL glmGamPoi
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘glmGamPoi’ ...
** this is package ‘glmGamPoi’ version ‘1.20.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++17
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c beta_estimation.cpp -o beta_estimation.o
beta_estimation.cpp: In function ‘bool lte_n_equal_rows(const Rcpp::NumericMatrix&, int, double)’:
beta_estimation.cpp:31:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   31 |   for(size_t row_idx = 0; row_idx < matrix.nrow(); row_idx++){
      |                           ~~~~~~~~^~~~~~~~~~~~~~~
beta_estimation.cpp:43:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   43 |       if(n_matches > n){
      |          ~~~~~~~~~~^~~
beta_estimation.cpp: In function ‘Rcpp::IntegerVector get_row_groups(const Rcpp::NumericMatrix&, int, double)’:
beta_estimation.cpp:57:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   57 |   for(size_t row_idx = 0; row_idx < matrix.nrow(); row_idx++){
      |                           ~~~~~~~~^~~~~~~~~~~~~~~
In file included from beta_estimation.cpp:5:
../inst/include/deviance.h: In instantiation of ‘arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]’:
../inst/include/deviance.h:88:58:   required from here
   88 |     return compute_gp_deviance_residuals_matrix_impl<int>(Y, Mu, thetas);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   76 |   for(int i = 0; i < Y.n_elem; i++){
      |                  ~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of ‘arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = double; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]’:
../inst/include/deviance.h:91:61:   required from here
   91 |     return compute_gp_deviance_residuals_matrix_impl<double>(Y, Mu, thetas);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   76 |   for(int i = 0; i < Y.n_elem; i++){
      |                  ~~^~~~~~~~~~
beta_estimation.cpp: In instantiation of ‘void clamp_inplace(arma::Mat<eT>&, double, double) [with NumericType = double]’:
beta_estimation.cpp:80:16:   required from here
   80 |   clamp_inplace(mu_hat, 1e-50, 1e50);
      |   ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
beta_estimation.cpp:14:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   14 |   for(int i = 0; i < v.n_elem; i++){
      |                  ~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of ‘double compute_gp_deviance_sum(const arma::Mat<eT>&, const arma::Mat<double>&, double) [with NumericType = double]’:
beta_estimation.cpp:256:40:   required from here
  256 |       dev_old = compute_gp_deviance_sum(counts, mu_hat, thetas(gene_idx)) + pen_sum;
      |                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/deviance.h:53:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   53 |   for (int i = 0; i < Y.n_elem; i++) {
      |                   ~~^~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c deviance.cpp -o deviance.o
In file included from deviance.cpp:3:
../inst/include/deviance.h: In instantiation of ‘arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]’:
../inst/include/deviance.h:88:58:   required from here
   88 |     return compute_gp_deviance_residuals_matrix_impl<int>(Y, Mu, thetas);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   76 |   for(int i = 0; i < Y.n_elem; i++){
      |                  ~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of ‘arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = double; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]’:
../inst/include/deviance.h:91:61:   required from here
   91 |     return compute_gp_deviance_residuals_matrix_impl<double>(Y, Mu, thetas);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   76 |   for(int i = 0; i < Y.n_elem; i++){
      |                  ~~^~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c overdispersion.cpp -o overdispersion.o
overdispersion.cpp: In function ‘Rcpp::List make_table_if_small(const Rcpp::NumericVector&, int)’:
overdispersion.cpp:25:22: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<long int, long unsigned int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   25 |     if(counts.size() > stop_if_larger){
      |        ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
overdispersion.cpp: In function ‘double conventional_loglikelihood_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const arma::mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)’:
overdispersion.cpp:92:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   92 |     for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
      |                          ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:100:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  100 |   for(size_t i = 0; i < y.size(); ++i){
      |                     ~~^~~~~~~~~~
overdispersion.cpp: In function ‘double conventional_score_function_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const arma::mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)’:
overdispersion.cpp:136:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  136 |     for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
      |                          ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:159:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  159 |     for(size_t iter = 0; iter < y.size(); ++iter){
      |                          ~~~~~^~~~~~~~~~
overdispersion.cpp:177:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  177 |   for(size_t i = 0; i < y.size(); ++i){
      |                     ~~^~~~~~~~~~
overdispersion.cpp: In function ‘double conventional_deriv_score_function_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const arma::mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)’:
overdispersion.cpp:233:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  233 |     for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
      |                          ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:251:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  251 |   for(size_t i = 0; i < y.size(); ++i){
      |                     ~~^~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c utils.cpp -o utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o glmGamPoi.so RcppExports.o beta_estimation.o deviance.o overdispersion.o utils.o -L/home/biocbuild/R/R/lib -lRlapack -L/home/biocbuild/R/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-glmGamPoi/00new/glmGamPoi/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 (glmGamPoi)