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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/4.4-x86_64/Resources/library’
* installing *source* package ‘miloR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp:237:9: warning: variable 'stot' set but not used [-Wunused-but-set-variable]
    int stot = 0;
        ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
fitGeneticPLGlmm.cpp:197:10: warning: unused variable '_phi_est' [-Wunused-variable]
    bool _phi_est = true; // control if we re-estimate phi or not
         ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c fitPLGlmm.cpp -o fitPLGlmm.o
fitPLGlmm.cpp:177:10: warning: unused variable '_phi_est' [-Wunused-variable]
    bool _phi_est = true; // control if we re-estimate phi or not
         ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c inference.cpp -o inference.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c invertPseudoVar.cpp -o invertPseudoVar.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c multiP.cpp -o multiP.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c paramEst.cpp -o paramEst.o
paramEst.cpp:29:33: warning: left operand of comma operator has no effect [-Wunused-value]
        double rhs = 0.5 * mid1[0, 0];
                                ^
paramEst.cpp:252:18: warning: unused variable 'i' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                 ^
paramEst.cpp:252:21: warning: unused variable 'j' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                    ^
paramEst.cpp:253:12: warning: unused variable '_ycovij' [-Wunused-variable]
    double _ycovij; // Declare temp_value
           ^
paramEst.cpp:294:18: warning: unused variable 'i' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                 ^
paramEst.cpp:294:21: warning: unused variable 'j' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                    ^
paramEst.cpp:295:12: warning: unused variable '_ycovij' [-Wunused-variable]
    double _ycovij; // Declare temp_value
           ^
paramEst.cpp:373:18: warning: unused variable 'i' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                 ^
paramEst.cpp:373:21: warning: unused variable 'j' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                    ^
paramEst.cpp:374:12: warning: unused variable '_ycovij' [-Wunused-variable]
    double _ycovij; // Declare temp_value
           ^
paramEst.cpp:484:18: warning: unused variable 'i' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                 ^
paramEst.cpp:484:21: warning: unused variable 'j' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                    ^
paramEst.cpp:485:12: warning: unused variable '_ycovij' [-Wunused-variable]
    double _ycovij; // Declare temp_value
           ^
paramEst.cpp:543:18: warning: variable 'inner_count' set but not used [-Wunused-but-set-variable]
    unsigned int inner_count = 0;
                 ^
paramEst.cpp:544:18: warning: unused variable 'outer_count' [-Wunused-variable]
    unsigned int outer_count = 0;
                 ^
paramEst.cpp:688:9: warning: unused variable 'j' [-Wunused-variable]
    int j, k, l, a;
        ^
paramEst.cpp:688:12: warning: unused variable 'k' [-Wunused-variable]
    int j, k, l, a;
           ^
paramEst.cpp:688:15: warning: unused variable 'l' [-Wunused-variable]
    int j, k, l, a;
              ^
paramEst.cpp:688:18: warning: unused variable 'a' [-Wunused-variable]
    int j, k, l, a;
                 ^
paramEst.cpp:866:12: warning: unused variable 'half_logli' [-Wunused-variable]
    double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
           ^
paramEst.cpp:871:10: warning: unused variable 'comp_vals' [-Wunused-variable]
    bool comp_vals = false;
         ^
21 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c pseudovarPartial.cpp -o pseudovarPartial.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c utils.cpp -o utils.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/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)