* installing *source* package ‘tidypopgen’ ... ** this is package ‘tidypopgen’ version ‘0.3.1’ ** using staged installation ** libs using C++ compiler: ‘Debian clang version 19.1.7 (3+b1)’ clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c RcppExports.cpp -o RcppExports.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c alt_freq_dip_pseudo_cpp.cpp -o alt_freq_dip_pseudo_cpp.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c compute_np_mn.cpp -o compute_np_mn.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c fbm_prod_and_rowSumSq.cpp -o fbm_prod_and_rowSumSq.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c grouped_alt_freq_dip_pseudo_cpp.cpp -o grouped_alt_freq_dip_pseudo_cpp.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c grouped_missingness_cpp.cpp -o grouped_missingness_cpp.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c grouped_summaries_dip_pseudo_cpp.cpp -o grouped_summaries_dip_pseudo_cpp.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c gt_grouped_pi_diploid.cpp -o gt_grouped_pi_diploid.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c gt_ind_hetero.cpp -o gt_ind_hetero.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c gt_pi_diploid.cpp -o gt_pi_diploid.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c hwe.cpp -o hwe.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c pairwise_fst_hudson_loop.cpp -o pairwise_fst_hudson_loop.o pairwise_fst_hudson_loop.cpp:44:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] 44 | int count = 0; | ^ 1 warning generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c pairwise_fst_nei87_loop.cpp -o pairwise_fst_nei87_loop.o pairwise_fst_nei87_loop.cpp:95:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] 95 | int count = 0; | ^ 1 warning generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c pairwise_fst_wc84_loop.cpp -o pairwise_fst_wc84_loop.o pairwise_fst_wc84_loop.cpp:102:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] 102 | int count = 0; | ^ 1 warning generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c read_packedancestry.cpp -o read_packedancestry.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c snp_as.cpp -o snp_as.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c snp_ibs.cpp -o snp_ibs.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c snp_king.cpp -o snp_king.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c vcf_parser_fast.cpp -o vcf_parser_fast.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rmio/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c write_to_FBM.cpp -o write_to_FBM.o clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -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 -llapack -L/home/hornik/tmp/R/lib -lRblas -L/usr/lib/llvm-19/lib -lFortranRuntime -lFortranDecimal -lm -lz -L/home/hornik/tmp/R/lib -lR installing to /srv/hornik/tmp/CRAN_pretest/tidypopgen.Rcheck/00LOCK-tidypopgen/00new/tidypopgen/libs ** 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)