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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL scDDboost
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘scDDboost’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c DATA.cpp -o DATA.o
DATA.cpp: In member function ‘std::vector<Eigen::Matrix<double, -1, -1> > DATA::reorg(Eigen::MatrixXd&, const VectorXi&)’:
DATA.cpp:17:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   17 |         for(int j = 0; j < s.size(); ++j){
      |                        ~~^~~~~~~~~~
DATA.cpp: In member function ‘std::vector<Eigen::Matrix<double, -1, -1> > DATA::reorgr(const MatrixXd&, const VectorXi&)’:
DATA.cpp:32:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   32 |         for(int j = 0; j < s.size(); ++j){
      |                        ~~^~~~~~~~~~
DATA.cpp: In member function ‘r_q DATA::cal_r(Eigen::MatrixXd&, const VectorXi&, const VectorXd&)’:
DATA.cpp:48:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   48 |     for(int i = 0; i < G; i++){
      |                    ~~^~~
DATA.cpp:49:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   49 |         for(int j = 0; j < nc; j++){
      |                        ~~^~~~
DATA.cpp:58:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   58 |     for(int i = 0; i < G; i++)
      |                    ~~^~~
DATA.cpp:59:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   59 |         for(int j = 0; j < K; j++){
      |                        ~~^~~
DATA.cpp:65:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   65 |             for(int t = 0; t < s.size(); t++)
      |                            ~~^~~~~~~~~~
DATA.cpp:70:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   70 |             for(int t = 0; t < s.size(); t++)
      |                            ~~^~~~~~~~~~
DATA.cpp:85:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   85 |     for(int i = 0; i < G; ++i){
      |                    ~~^~~
DATA.cpp: In member function ‘Eigen::MatrixXd DATA::cal_hp()’:
DATA.cpp:106:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  106 |     for(int j=0;j<K;++j){
      |                 ~^~
DATA.cpp:113:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  113 |     for(int i=0;i<G;++i){
      |                 ~^~
DATA.cpp:114:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  114 |         for(int j=0;j<K;++j){
      |                     ~^~
DATA.cpp: In constructor ‘DATA::DATA(Eigen::MatrixXd&, const VectorXi&, const VectorXd&, const MatrixXi&)’:
DATA.cpp:157:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  157 |     for(int j=0;j<K;j++){
      |                 ~^~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Header.cpp -o Header.o
Header.cpp: In function ‘std::vector<std::vector<int> > partition(const int&)’:
Header.cpp:38:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   38 |         for(int j=0;j<L;++j){
      |                     ~^~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c derived.cpp -o derived.o
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/constants/constants.hpp:14,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:20,
                 from derived.h:14,
                 from derived.cpp:9:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
derived.cpp: In constructor ‘DC::DC(Eigen::MatrixXd&, Eigen::VectorXi&, Eigen::VectorXd&, std::vector<int>&, Eigen::MatrixXi&)’:
derived.cpp:31:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   31 |         for(int j = 0; j < K; j++){
      |                        ~~^~~
derived.cpp: In member function ‘void DC::go_drv(const MatrixXd&, const MatrixXd&, double&, Eigen::VectorXd&, double, double)’:
derived.cpp:162:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  162 |     for(int i = 0; i < G; i++)
      |                    ~~^~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c main.cpp -o main.o
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/constants/constants.hpp:14,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:20,
                 from derived.h:14,
                 from main.cpp:21:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
main.cpp: In function ‘SEXPREC* new_D(SEXP, SEXP, SEXP)’:
main.cpp:217:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  217 |     for(int i=0;i<de_i.size();i++){
      |                 ~^~~~~~~~~~~~
main.cpp:228:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  228 |     for(int i=0;i<cd.size();i++){
      |                 ~^~~~~~~~~~
main.cpp:229:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  229 |         for(int j=i+1;j<cd.size();j++){
      |                       ~^~~~~~~~~~
main.cpp:231:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  231 |             for(int t=0;t<de_i.size();t++){
      |                         ~^~~~~~~~~~~~
main.cpp: In function ‘SEXPREC* pat(SEXP)’:
main.cpp:283:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  283 |     for(int i=0;i<res.size();i++)
      |                 ~^~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c scDDboost_init.c -o scDDboost_init.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o scDDboost.so DATA.o Header.o derived.o main.o scDDboost_init.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-scDDboost/00new/scDDboost/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (scDDboost)