* installing *source* package ‘tidypopgen’ ...
** this is package ‘tidypopgen’ version ‘0.3.2’
** package ‘tidypopgen’ 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)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -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'/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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c alt_freq_dip_pseudo_cpp.cpp -o alt_freq_dip_pseudo_cpp.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c compute_np_mn.cpp -o compute_np_mn.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c fbm_prod_and_rowSumSq.cpp -o fbm_prod_and_rowSumSq.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c grouped_alt_freq_dip_pseudo_cpp.cpp -o grouped_alt_freq_dip_pseudo_cpp.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c grouped_missingness_cpp.cpp -o grouped_missingness_cpp.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c grouped_summaries_dip_pseudo_cpp.cpp -o grouped_summaries_dip_pseudo_cpp.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c gt_grouped_pi_diploid.cpp -o gt_grouped_pi_diploid.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c gt_ind_hetero.cpp -o gt_ind_hetero.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c gt_pi_diploid.cpp -o gt_pi_diploid.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c hwe.cpp -o hwe.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c pairwise_fst_hudson_loop.cpp -o pairwise_fst_hudson_loop.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c pairwise_fst_nei87_loop.cpp -o pairwise_fst_nei87_loop.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c pairwise_fst_wc84_loop.cpp -o pairwise_fst_wc84_loop.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c read_packedancestry.cpp -o read_packedancestry.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c snp_as.cpp -o snp_as.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c snp_ibs.cpp -o snp_ibs.o
pairwise_fst_hudson_loop.cpp:44:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count = 0;
^
pairwise_fst_nei87_loop.cpp:95:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count = 0;
^
pairwise_fst_wc84_loop.cpp:102:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count = 0;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c snp_king.cpp -o snp_king.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c vcf_parser_fast.cpp -o vcf_parser_fast.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/bigstatsr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmio/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c write_to_FBM.cpp -o write_to_FBM.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 tidypopgen.so RcppExports.o alt_freq_dip_pseudo_cpp.o compute_np_mn.o fbm_prod_and_rowSumSq.o grouped_alt_freq_dip_pseudo_cpp.o grouped_missingness_cpp.o grouped_summaries_dip_pseudo_cpp.o gt_grouped_pi_diploid.o gt_ind_hetero.o gt_pi_diploid.o hwe.o pairwise_fst_hudson_loop.o pairwise_fst_nei87_loop.o pairwise_fst_wc84_loop.o read_packedancestry.o snp_as.o snp_ibs.o snp_king.o vcf_parser_fast.o write_to_FBM.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 -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.5/tidypopgen.Rcheck/00LOCK-tidypopgen/00new/tidypopgen/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
*** 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 (tidypopgen)