* installing *source* package ‘adapt3’ ...
** this is package ‘adapt3’ version ‘2.0.7’
** package ‘adapt3’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
Warning in system2("xcrun", "--show-sdk-version", TRUE, TRUE) :
  running command ''xcrun' --show-sdk-version 2>&1' had status 1
using SDK: ‘NA’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/lefko3/include' -I/opt/R/x86_64/include   -I../inst/include/ -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 -DARMA_64BIT_WORD=1 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/lefko3/include' -I/opt/R/x86_64/include   -I../inst/include/ -fPIC  -falign-functions=64 -Wall -g -O2   -c projection.cpp -o projection.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/lefko3/include' -I/opt/R/x86_64/include   -I../inst/include/ -fPIC  -falign-functions=64 -Wall -g -O2   -c utilities.cpp -o utilities.o
In file included from utilities.cpp:7:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/lefko3/include/LefkoUtils.h:8:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/lefko3/include/basic_funcs/mat_stuff.h:1672:12: warning: variable 'esta2_used' set but not used [-Wunused-but-set-variable]
      bool esta2_used {false};
           ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/lefko3/include/basic_funcs/mat_stuff.h:1478:9: warning: variable 'age_related_stages' set but not used [-Wunused-but-set-variable]
    int age_related_stages {0};
        ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/lefko3/include/basic_funcs/mat_stuff.h:1479:9: warning: variable 'age_related_min_ages' set but not used [-Wunused-but-set-variable]
    int age_related_min_ages {0};
        ^
In file included from projection.cpp:10:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/lefko3/include/LefkoUtils.h:8:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/lefko3/include/basic_funcs/mat_stuff.h:1672:12: warning: variable 'esta2_used' set but not used [-Wunused-but-set-variable]
      bool esta2_used {false};
           ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/lefko3/include/basic_funcs/mat_stuff.h:1478:9: warning: variable 'age_related_stages' set but not used [-Wunused-but-set-variable]
    int age_related_stages {0};
        ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/lefko3/include/basic_funcs/mat_stuff.h:1479:9: warning: variable 'age_related_min_ages' set but not used [-Wunused-but-set-variable]
    int age_related_min_ages {0};
        ^
In file included from utilities.cpp:8:
In file included from ../inst/include/AdaptUtils.h:7:
../inst/include/basic_funcs/main_utils.h:4474:9: warning: variable 'good_max_age_values' set but not used [-Wunused-but-set-variable]
    int good_max_age_values {0};
        ^
In file included from projection.cpp:11:
In file included from ../inst/include/AdaptUtils.h:7:
../inst/include/basic_funcs/main_utils.h:4474:9: warning: variable 'good_max_age_values' set but not used [-Wunused-but-set-variable]
    int good_max_age_values {0};
        ^
In file included from utilities.cpp:8:
In file included from ../inst/include/AdaptUtils.h:8:
../inst/include/basic_funcs/mats_utils.h:3699:9: warning: unused variable 'nostages_nounborn' [-Wunused-variable]
    int nostages_nounborn = nostages - almostbornstages;
        ^
In file included from projection.cpp:11:
In file included from ../inst/include/AdaptUtils.h:8:
../inst/include/basic_funcs/mats_utils.h:3699:9: warning: unused variable 'nostages_nounborn' [-Wunused-variable]
    int nostages_nounborn = nostages - almostbornstages;
        ^
projection.cpp:5880:8: warning: variable 'pure_fleslie' set but not used [-Wunused-but-set-variable]
  bool pure_fleslie {false}; // Are all function-based MPMs Leslie MPMs?
       ^
projection.cpp:5885:7: warning: variable 'stageframe_count' set but not used [-Wunused-but-set-variable]
  int stageframe_count {0};
      ^
projection.cpp:5886:7: warning: variable 'stageframe_notNull_count' set but not used [-Wunused-but-set-variable]
  int stageframe_notNull_count {0};
      ^
projection.cpp:5887:7: warning: variable 'supplement_count' set but not used [-Wunused-but-set-variable]
  int supplement_count {0};
      ^
projection.cpp:5888:7: warning: variable 'equivalence_count' set but not used [-Wunused-but-set-variable]
  int equivalence_count {0};
      ^
projection.cpp:5889:7: warning: variable 'start_count' set but not used [-Wunused-but-set-variable]
  int start_count {0};
      ^
projection.cpp:5890:7: warning: variable 'tweights_count' set but not used [-Wunused-but-set-variable]
  int tweights_count {0};
      ^
projection.cpp:5891:7: warning: variable 'density_count' set but not used [-Wunused-but-set-variable]
  int density_count {0};
      ^
projection.cpp:5892:7: warning: variable 'entry_time_count' set but not used [-Wunused-but-set-variable]
  int entry_time_count {0};
      ^
projection.cpp:5893:7: warning: variable 'density_vr_count' set but not used [-Wunused-but-set-variable]
  int density_vr_count {0};
      ^
projection.cpp:5894:7: warning: variable 'sparse_vec_count' set but not used [-Wunused-but-set-variable]
  int sparse_vec_count {0};
      ^
projection.cpp:5895:7: warning: variable 'found_fleslie' set but not used [-Wunused-but-set-variable]
  int found_fleslie {0};
      ^
projection.cpp:7874:15: warning: variable 'maxage_NAs' set but not used [-Wunused-but-set-variable]
          int maxage_NAs {0};
              ^
projection.cpp:6582:8: warning: unused variable 'sensitivity_bool' [-Wunused-variable]
  bool sensitivity_bool {false};
       ^
projection.cpp:12838:18: warning: unused variable 'res_fitness_test' [-Wunused-variable]
          double res_fitness_test = current_round_fitness_values(0);
                 ^
projection.cpp:12468:12: warning: variable 'conv_test' set but not used [-Wunused-but-set-variable]
    double conv_test {0.};
           ^
projection.cpp:12470:12: warning: variable 'xE' set but not used [-Wunused-but-set-variable]
    double xE {0.}; // test value to keep in memory from previous expansion round
           ^
projection.cpp:12471:12: warning: variable 'xC_new' set but not used [-Wunused-but-set-variable]
    double xC_new {0.}; // test value to keep in memory from previous contraction round
           ^
projection.cpp:13053:7: warning: unused variable 'optim_rows' [-Wunused-variable]
  int optim_rows = static_cast<int>(final_output_df.nrows());
      ^
projection.cpp:14893:18: warning: unused variable 'res_fitness_test' [-Wunused-variable]
          double res_fitness_test = current_round_fitness_values(0);
                 ^
projection.cpp:14411:12: warning: variable 'conv_test' set but not used [-Wunused-but-set-variable]
    double conv_test {0.};
           ^
projection.cpp:14413:12: warning: variable 'xE' set but not used [-Wunused-but-set-variable]
    double xE {0.}; // test value to keep in memory from previous expansion round
           ^
projection.cpp:14414:12: warning: variable 'xC_new' set but not used [-Wunused-but-set-variable]
    double xC_new {0.}; // test value to keep in memory from previous contraction round
           ^
projection.cpp:15110:7: warning: unused variable 'optim_rows' [-Wunused-variable]
  int optim_rows = static_cast<int>(final_output_df.nrows());
      ^
projection.cpp:19851:7: warning: unused variable 'stageframe_count' [-Wunused-variable]
  int stageframe_count {0};
      ^
projection.cpp:19852:7: warning: variable 'stageframe_notNull_count' set but not used [-Wunused-but-set-variable]
  int stageframe_notNull_count {0};
      ^
projection.cpp:19853:7: warning: unused variable 'supplement_count' [-Wunused-variable]
  int supplement_count {0};
      ^
projection.cpp:19854:7: warning: variable 'equivalence_count' set but not used [-Wunused-but-set-variable]
  int equivalence_count {0};
      ^
projection.cpp:19855:7: warning: variable 'start_count' set but not used [-Wunused-but-set-variable]
  int start_count {0};
      ^
projection.cpp:19856:7: warning: variable 'tweights_count' set but not used [-Wunused-but-set-variable]
  int tweights_count {0};
      ^
projection.cpp:19857:7: warning: variable 'density_count' set but not used [-Wunused-but-set-variable]
  int density_count {0};
      ^
projection.cpp:19859:7: warning: variable 'entry_time_count' set but not used [-Wunused-but-set-variable]
  int entry_time_count {0};
      ^
projection.cpp:19860:7: warning: variable 'density_vr_count' set but not used [-Wunused-but-set-variable]
  int density_vr_count {0};
      ^
projection.cpp:19861:7: warning: variable 'sparse_vec_count' set but not used [-Wunused-but-set-variable]
  int sparse_vec_count {0};
      ^
projection.cpp:19873:8: warning: variable 'prebreeding_bool' set but not used [-Wunused-but-set-variable]
  bool prebreeding_bool {true};
       ^
5 warnings generated.
40 warnings generated.
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 adapt3.so RcppExports.o projection.o utilities.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-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.5/adapt3.Rcheck/00LOCK-adapt3/00new/adapt3/libs
** generating debug symbols (dSYM)
** R
** data
*** moving datasets to lazyload DB
** 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 (adapt3)