* installing *source* package ‘poppr’ ...
** package ‘poppr’ successfully unpacked and MD5 sums checked
** 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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c adjust_missing.c -o adjust_missing.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bitwise_distance.c -o bitwise_distance.o
bitwise_distance.c:162:7: warning: variable 'num_threads' set but not used [-Wunused-but-set-variable]
  int num_threads;
      ^
bitwise_distance.c:495:7: warning: variable 'num_threads' set but not used [-Wunused-but-set-variable]
  int num_threads;
      ^
bitwise_distance.c:815:7: warning: variable 'chr_length' set but not used [-Wunused-but-set-variable]
  int chr_length;
      ^
bitwise_distance.c:808:8: warning: unused variable 'R_chr2_1' [-Wunused-variable]
  SEXP R_chr2_1;
       ^
bitwise_distance.c:824:7: warning: variable 'num_threads' set but not used [-Wunused-but-set-variable]
  int num_threads;
      ^
bitwise_distance.c:823:7: warning: unused variable 'only_differences' [-Wunused-variable]
  int only_differences;
      ^
bitwise_distance.c:1199:7: warning: variable 'num_threads' set but not used [-Wunused-but-set-variable]
  int num_threads;
      ^
bitwise_distance.c:1182:8: warning: unused variable 'R_chr2_2' [-Wunused-variable]
  SEXP R_chr2_2;
       ^
bitwise_distance.c:1181:8: warning: unused variable 'R_chr2_1' [-Wunused-variable]
  SEXP R_chr2_1;
       ^
bitwise_distance.c:1190:7: warning: variable 'chr_length' set but not used [-Wunused-but-set-variable]
  int chr_length;
      ^
10 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mlg_clustering.c -o mlg_clustering.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mlg_counter.c -o mlg_counter.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c msn.c -o msn.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c omp_test.c -o omp_test.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c permut_shuffler.c -o permut_shuffler.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c poppr_distance.c -o poppr_distance.o
poppr_distance.c:428:6: warning: variable 'numel' set but not used [-Wunused-but-set-variable]
        int numel; // Number of elements in returned matrix
            ^
1 warning generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o poppr.so adjust_missing.o bitwise_distance.o init.o mlg_clustering.o mlg_counter.o msn.o omp_test.o permut_shuffler.o poppr_distance.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.3/poppr.Rcheck/00LOCK-poppr/00new/poppr/libs
** generating debug symbols (dSYM)
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘as.genambig’ in package ‘poppr’
** help
*** installing help indices
*** copying figures
** 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 (poppr)