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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL EBSeq
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘EBSeq’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Rexport.cpp -o Rexport.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/tools/series.hpp:16,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:17,
                 from agglomerativeClustering.hpp:9,
                 from negativeBinomial.hpp:5,
                 from Rexport.cpp:11:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigen.h:25,
                 from Rexport.cpp:2:
/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]':
/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]':
/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
In file included from Rexport.cpp:5:
partition.hpp: In static member function 'static std::vector<std::vector<int> > EBS::partition::Part(int)':
partition.hpp:26:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   26 |                 for(int j = 0;j < L; ++j){
      |                               ~~^~~
partition.hpp: In static member function 'static std::vector<std::vector<int> > EBS::partition::monoPart(int)':
partition.hpp:53:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   53 |                 for(int j = 0;j < L; ++j){
      |                               ~~^~~
partition.hpp: In static member function 'static std::vector<int> EBS::partition::reorder(std::vector<int>&)':
partition.hpp:155:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  155 |                 for(int j = 0; j < K; j++)
      |                                ~~^~~
partition.hpp: In static member function 'static EBS::COUNTS EBS::partition::toMatrix(std::vector<int>&)':
partition.hpp:208:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  208 |                 for(int j = 0; j < K; j++)
      |                                ~~^~~
In file included from Rexport.cpp:7:
aggregate.hpp: In static member function 'static EBS::COUNTS EBS::aggregate::sum(Eigen::VectorXd&, EBS::CLUSINFO&)':
aggregate.hpp:24:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   24 |         for(auto i = 0; i < K; i++)
      |                         ~~^~~
aggregate.hpp: In static member function 'static EBS::COUNTS EBS::aggregate::sum(EBS::COUNTS&, EBS::CLUSINFO&)':
aggregate.hpp:43:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   43 |         for(auto i = 0; i < K; i++)
      |                         ~~^~~
aggregate.hpp: In static member function 'static EBS::COUNTS EBS::aggregate::sum(EBS::COUNTS&, EBS::CLUSINFO&, Eigen::VectorXd&)':
aggregate.hpp:62:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   62 |         for(auto i = 0; i < K; i++)
      |                         ~~^~~
aggregate.hpp: In static member function 'static EBS::COUNTS EBS::aggregate::groupMean(EBS::COUNTS, EBS::CLUSINFO&)':
aggregate.hpp:77:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   77 |         for(auto i = 0; i < K; i++)
      |                         ~~^~~
aggregate.hpp: In static member function 'static EBS::COUNTS EBS::aggregate::groupVar(EBS::COUNTS&, EBS::COUNTS&, EBS::CLUSINFO&)':
aggregate.hpp:101:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  101 |         for(int i = 0; i < K; i++)
      |                        ~~^~~
aggregate.hpp: In static member function 'static EBS::COUNTS EBS::aggregate::groupVar(EBS::COUNTS&, EBS::COUNTS&, EBS::CLUSINFO&, Eigen::VectorXd&)':
aggregate.hpp:122:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  122 |         for(int i = 0; i < K; i++)
      |                        ~~^~~
negativeBinomial.hpp: In constructor 'EBS::NB::NB(EBS::COUNTS&, std::vector<int>&, Eigen::VectorXd&, std::vector<std::vector<int> >&)':
negativeBinomial.hpp:32:38: warning: comparison of integer expressions of different signedness: 'Eigen::Index' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   32 |             if(scRNAexpMatrix.cols() > nk)
      |                ~~~~~~~~~~~~~~~~~~~~~~^~~~
negativeBinomial.hpp:59:41: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare]
   59 |                     for(size_t j = 0; j < _mean.cols(); j++)
      |                                       ~~^~~~~~~~~~~~~~
negativeBinomial.hpp:93:51: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare]
   93 |                         for(size_t iter = 0; iter < _sum.rows(); iter++)
      |                                              ~~~~~^~~~~~~~~~~~~
negativeBinomial.hpp:115:51: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare]
  115 |                         for(size_t iter = 0; iter < _sum.rows(); iter++)
      |                                              ~~~~~^~~~~~~~~~~~~
negativeBinomial.hpp:139:26: warning: variable 'maxholder' set but not used [-Wunused-but-set-variable]
  139 |                     auto maxholder = add.maxCoeff(&maxRow, &maxCol);
      |                          ^~~~~~~~~
negativeBinomial.hpp:160:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase<Eigen::Array<double, -1, 1> >::Index' {aka 'long int'} [-Wsign-compare]
  160 |                 for(size_t useRow = 0; useRow < use.size(); useRow++)
      |                                        ~~~~~~~^~~~~~~~~~~~
negativeBinomial.hpp:180:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase<Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, const Eigen::ArrayWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double, double>, const Eigen::Matrix<double, -1, -1>, const Eigen::Matrix<double, -1, 1> > >, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::ArrayWrapper<Eigen::Matrix<double, -1, 1> >, const Eigen::ArrayWrapper<Eigen::Matrix<double, -1, 1> > > > >::Index' {aka 'long int'} [-Wsign-compare]
  180 |                 for(size_t iter = 0; iter < phi.size(); iter++)
      |                                      ~~~~~^~~~~~~~~~~~
negativeBinomial.hpp: In member function 'void EBS::NB::init(EBS::Float, Eigen::VectorXd, std::vector<int>, std::vector<double>, int, EBS::Float, EBS::Float, EBS::Float, int)':
negativeBinomial.hpp:242:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare]
  242 |             if(_ng < _sum.rows())
      |                ~~~~^~~~~~~~~~~~~
negativeBinomial.hpp:250:43: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  250 |                         if(_isoLabel[pos] == lab)
negativeBinomial.hpp: In member function 'void EBS::NB::equalHandle(std::vector<bool>&, std::vector<double>&, Eigen::VectorXd&, Eigen::VectorXd&, EBS::Float&, EBS::Float&, EBS::Float&, EBS::Float&, std::vector<int>&, int, int)':
negativeBinomial.hpp:803:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  803 |             while(pos < baseBit.size())
      |                   ~~~~^~~~~~~~~~~~~~~~
Rexport.cpp: In function 'SEXPREC* EBSeq(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Rexport.cpp:84:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
   84 |     for(size_t i = 0; i < nr; i++){
      |                       ~~^~~~
Rexport.cpp:85:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
   85 |         for(size_t j = 0; j < nk; j++){
      |                           ~~^~~~
Rexport.cpp:150:28: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare]
  150 |     for (size_t ri = 0; ri < mDep.rows(); ri++)
      |                         ~~~^~~~~~~~~~~~~
Rexport.cpp:151:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare]
  151 |         for(size_t ci = 0; ci < mDep.cols(); ci++)
      |                            ~~~^~~~~~~~~~~~~
Rexport.cpp: In function 'SEXPREC* EBSeqWQ(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Rexport.cpp:275:28: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare]
  275 |     for (size_t ri = 0; ri < mDep.rows(); ri++)
      |                         ~~~^~~~~~~~~~~~~
Rexport.cpp:276:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare]
  276 |         for(size_t ci = 0; ci < mDep.cols(); ci++)
      |                            ~~~^~~~~~~~~~~~~
agglomerativeClustering.hpp: In instantiation of 'static void EBS::ALGO::hclust(ROW&, ROW&, std::vector<double>&, int, int, EBS::Float, EBS::Float, EBS::Float, EBS::Float, std::vector<int>&) [with ROW = Eigen::Matrix<double, -1, 1>; EBS::Float = double]':
negativeBinomial.hpp:818:51:   required from here
  818 |                         ALGO::hclust<Eigen::VectorXd>(cs,rs,logRatio,start,pos,
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
  819 |                                      alpha,beta,th1,th2,sz);
      |                                      ~~~~~~~~~~~~~~~~~~~~~~
agglomerativeClustering.hpp:87:37: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   87 |                 for(size_t i = 0; i < counter; i++)
      |                                   ~~^~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o EBSeq.so Rexport.o -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-EBSeq/00new/EBSeq/libs
** R
** data
** demo
** 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 (EBSeq)