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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miloR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘miloR’ ...
** this is package ‘miloR’ version ‘2.7.2’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -fPIC  -falign-functions=64 -Wall -g -O2   -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp:246:9: warning: variable 'stot' set but not used [-Wunused-but-set-variable]
  246 |     int stot = 0;
      |         ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -fPIC  -falign-functions=64 -Wall -g -O2   -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
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
      |          ^~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -fPIC  -falign-functions=64 -Wall -g -O2   -c fitPLGlmm.cpp -o fitPLGlmm.o
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
      |          ^~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -fPIC  -falign-functions=64 -Wall -g -O2   -c inference.cpp -o inference.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -fPIC  -falign-functions=64 -Wall -g -O2   -c invertPseudoVar.cpp -o invertPseudoVar.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -fPIC  -falign-functions=64 -Wall -g -O2   -c multiP.cpp -o multiP.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -fPIC  -falign-functions=64 -Wall -g -O2   -c paramEst.cpp -o paramEst.o
paramEst.cpp:36:34: warning: top-level comma expression in array subscript is deprecated in C++20 and unsupported in C++23 [-Wdeprecated-comma-subscript]
   36 |         double rhs = 0.5 * mid1[0, 0];
      |                            ~~~~~~^~~~
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: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: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: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: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:407:19: warning: unused variable 'nsq' [-Wunused-variable]
  407 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:408:18: warning: unused variable 'i' [-Wunused-variable]
  408 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:408:21: warning: unused variable 'j' [-Wunused-variable]
  408 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:439:19: warning: unused variable 'nsq' [-Wunused-variable]
  439 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:440:18: warning: unused variable 'i' [-Wunused-variable]
  440 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:440:21: warning: unused variable 'j' [-Wunused-variable]
  440 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:780:12: warning: unused variable 'half_logli' [-Wunused-variable]
  780 |     double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
      |            ^~~~~~~~~~
paramEst.cpp:785:10: warning: unused variable 'comp_vals' [-Wunused-variable]
  785 |     bool comp_vals = false;
      |          ^~~~~~~~~
23 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -fPIC  -falign-functions=64 -Wall -g -O2   -c pseudovarPartial.cpp -o pseudovarPartial.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -fPIC  -falign-functions=64 -Wall -g -O2   -c utils.cpp -o utils.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o miloR.so RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/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)