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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL miloR
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘miloR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
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 RcppExports.cpp:5:
/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
      |        ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp: In function 'arma::mat initialiseG(Rcpp::List, arma::vec)':
computeMatrices.cpp:144:30: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
  144 |     for(unsigned long k=0; k < stot; k++){
      |                            ~~^~~~~~
computeMatrices.cpp:152:28: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
  152 |             for(int l=0; l < q; l++){
      |                          ~~^~~
computeMatrices.cpp: In function 'arma::mat invGmat(Rcpp::List, arma::vec)':
computeMatrices.cpp:336:30: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
  336 |     for(unsigned long k=0; k < stot; k++){
      |                            ~~^~~~~~
computeMatrices.cpp:344:28: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
  344 |             for(int l=0; l < q; l++){
      |                          ~~^~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
fitGeneticPLGlmm.cpp: In function 'Rcpp::List fitGeneticPLGlmm(const arma::mat&, const arma::mat&, const arma::mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const arma::vec&, Rcpp::List, double, const Rcpp::List&, double, const bool&, const int&, std::string, std::string)':
fitGeneticPLGlmm.cpp:113:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
  113 |     double _intercept = constval; // intercept for HE regression
      |            ^~~~~~~~~~
fitGeneticPLGlmm.cpp:200:10: warning: unused variable '_phi_est' [-Wunused-variable]
  200 |     bool _phi_est = true; // control if we re-estimate phi or not
      |          ^~~~~~~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c fitPLGlmm.cpp -o fitPLGlmm.o
fitPLGlmm.cpp: In function 'Rcpp::List fitPLGlmm(const arma::mat&, const arma::mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const arma::vec&, Rcpp::List, double, const Rcpp::List&, double, const bool&, const int&, std::string, std::string)':
fitPLGlmm.cpp:106:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
  106 |     double _intercept = constval; // intercept for HE regression?? need a better estimate.
      |            ^~~~~~~~~~
fitPLGlmm.cpp:172:10: warning: unused variable '_phi_est' [-Wunused-variable]
  172 |     bool _phi_est = true; // control if we re-estimate phi or not
      |          ^~~~~~~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c inference.cpp -o inference.o
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c invertPseudoVar.cpp -o invertPseudoVar.o
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c multiP.cpp -o multiP.o
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c paramEst.cpp -o paramEst.o
paramEst.cpp: In function 'arma::vec sigmaScoreREML_arma(const Rcpp::List&, const arma::vec&, const arma::mat&, const arma::vec&, const arma::mat&, const arma::mat&, const Rcpp::List&)':
paramEst.cpp:36:33: warning: left operand of comma operator has no effect [-Wunused-value]
   36 |         double rhs = 0.5 * mid1[0, 0];
      |                                 ^
paramEst.cpp: In function 'arma::vec solveEquations(const int&, const int&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::vec&, const arma::vec&, const arma::vec&)':
paramEst.cpp:172:12: warning: unused variable 'lambda' [-Wunused-variable]
  172 |     double lambda = 1e-1;
      |            ^~~~~~
paramEst.cpp:173:12: warning: unused variable 'lambda_step' [-Wunused-variable]
  173 |     double lambda_step = 10;
      |            ^~~~~~~~~~~
paramEst.cpp:174:12: warning: unused variable '_illcond_eps' [-Wunused-variable]
  174 |     double _illcond_eps = 1e-6;
      |            ^~~~~~~~~~~~
paramEst.cpp:175:12: warning: unused variable '_lcond_target' [-Wunused-variable]
  175 |     double _lcond_target = 1e-5;
      |            ^~~~~~~~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElstonGenetic(const arma::mat&, const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&)':
paramEst.cpp:241:19: warning: unused variable 'nsq' [-Wunused-variable]
  241 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix, no diag
      |                   ^~~
paramEst.cpp:242:18: warning: unused variable 'i' [-Wunused-variable]
  242 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:242:21: warning: unused variable 'j' [-Wunused-variable]
  242 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:243:12: warning: unused variable '_ycovij' [-Wunused-variable]
  243 |     double _ycovij; // Declare temp_value
      |            ^~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElston(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&)':
paramEst.cpp:276:19: warning: unused variable 'nsq' [-Wunused-variable]
  276 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:277:18: warning: unused variable 'i' [-Wunused-variable]
  277 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:277:21: warning: unused variable 'j' [-Wunused-variable]
  277 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:278:12: warning: unused variable '_ycovij' [-Wunused-variable]
  278 |     double _ycovij; // Declare temp_value
      |            ^~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElstonConstrained(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, arma::vec, const int&, const arma::mat&)':
paramEst.cpp:342:19: warning: unused variable 'nsq' [-Wunused-variable]
  342 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp: In function 'arma::vec estHasemanElstonConstrainedGenetic(const arma::mat&, const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&, arma::vec, const int&)':
paramEst.cpp:409:19: warning: unused variable 'nsq' [-Wunused-variable]
  409 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:410:18: warning: unused variable 'i' [-Wunused-variable]
  410 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:410:21: warning: unused variable 'j' [-Wunused-variable]
  410 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp: In function 'arma::vec estHasemanElstonConstrainedGeneticML(const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&, arma::vec, const int&)':
paramEst.cpp:442:19: warning: unused variable 'nsq' [-Wunused-variable]
  442 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:443:18: warning: unused variable 'i' [-Wunused-variable]
  443 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:443:21: warning: unused variable 'j' [-Wunused-variable]
  443 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp: In function 'arma::vec nnlsSolve(const arma::mat&, const arma::vec&, arma::vec, const int&)':
paramEst.cpp:478:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  478 |     for(int i=0; i < m; i++){
      |                  ~~^~~
paramEst.cpp:488:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  488 |     for(int i=0; i < m; i++){
      |                  ~~^~~
paramEst.cpp:515:24: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  515 |         for(int i=0; i < m; i++){
      |                      ~~^~~
paramEst.cpp:549:28: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  549 |             for(int i=0; i < m; i++){
      |                          ~~^~~
paramEst.cpp: In function 'double phiLineSearch(double, double, double, const int&, const arma::vec&, const arma::mat&, double, const arma::vec&, const arma::vec&, const arma::vec&)':
paramEst.cpp:774:12: warning: unused variable 'half_logli' [-Wunused-variable]
  774 |     double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
      |            ^~~~~~~~~~
paramEst.cpp:779:10: warning: unused variable 'comp_vals' [-Wunused-variable]
  779 |     bool comp_vals = false;
      |          ^~~~~~~~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c pseudovarPartial.cpp -o pseudovarPartial.o
pseudovarPartial.cpp: In function 'Rcpp::List computePZList(const Rcpp::List&, const arma::mat&, const arma::mat&, const arma::mat&, const std::string&)':
pseudovarPartial.cpp:51:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   51 |     for(int i=0; i < c; i++){
      |                  ~~^~~
pseudovarPartial.cpp: In function 'Rcpp::List computePZList_G(const Rcpp::List&, const arma::mat&, const arma::mat&, const arma::mat&, const std::string&, const arma::mat&)':
pseudovarPartial.cpp:73:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   73 |     for(int i=0; i < c; i++){
      |                  ~~^~~
pseudovarPartial.cpp:77:14: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   77 |         if(i == c - 1){
      |            ~~^~~~~~~~
pseudovarPartial.cpp: In function 'Rcpp::List pseudovarPartial_P(Rcpp::List, const arma::mat&)':
pseudovarPartial.cpp:108:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  108 |         for (int j = 0; j < n; j++) {
      |                         ~~^~~
pseudovarPartial.cpp:110:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  110 |             for (int k = 0; k < n; k++) {
      |                             ~~^~~
pseudovarPartial.cpp:113:32: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  113 |                 for(int a=0; a < n; a++){
      |                              ~~^~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c solveQP.cpp -o solveQP.o
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 /home/biocbuild/R/R-4.4.1/site-library/RcppML/include/RcppMLCommon.hpp:36,
                 from solveQP.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
      |        ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c utils.cpp -o utils.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o miloR.so RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o solveQP.o utils.o -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -fopenmp -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-miloR/00new/miloR/libs
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘graph’ in package ‘miloR’
** 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 (miloR)