* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* 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: ‘g++-14 (Debian 14.3.0-5) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpVmaovi/R.INSTALL1f4887104e61e1/tidypopgen/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from RcppExports.cpp:4:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c alt_freq_dip_pseudo_cpp.cpp -o alt_freq_dip_pseudo_cpp.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c compute_np_mn.cpp -o compute_np_mn.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c fbm_prod_and_rowSumSq.cpp -o fbm_prod_and_rowSumSq.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c grouped_alt_freq_dip_pseudo_cpp.cpp -o grouped_alt_freq_dip_pseudo_cpp.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c grouped_missingness_cpp.cpp -o grouped_missingness_cpp.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c grouped_summaries_dip_pseudo_cpp.cpp -o grouped_summaries_dip_pseudo_cpp.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c gt_grouped_pi_diploid.cpp -o gt_grouped_pi_diploid.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c gt_ind_hetero.cpp -o gt_ind_hetero.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c gt_pi_diploid.cpp -o gt_pi_diploid.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c hwe.cpp -o hwe.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c pairwise_fst_hudson_loop.cpp -o pairwise_fst_hudson_loop.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c pairwise_fst_nei87_loop.cpp -o pairwise_fst_nei87_loop.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c pairwise_fst_wc84_loop.cpp -o pairwise_fst_wc84_loop.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c read_packedancestry.cpp -o read_packedancestry.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c snp_as.cpp -o snp_as.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include/bigstatsr/arma-strict-R-headers.h:5,
from snp_as.cpp:3:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c snp_ibs.cpp -o snp_ibs.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include/bigstatsr/arma-strict-R-headers.h:5,
from snp_ibs.cpp:3:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c snp_king.cpp -o snp_king.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include/bigstatsr/arma-strict-R-headers.h:5,
from snp_king.cpp:3:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c vcf_parser_fast.cpp -o vcf_parser_fast.o
In function ‘bool gz_getline(gzFile, std::string&)’,
inlined from ‘bool vcf_genotypes_to_fbm(std::string, Rcpp::Environment, Rcpp::IntegerVector&, int, int)’ at vcf_parser_fast.cpp:309:17:
vcf_parser_fast.cpp:17:16: warning: ‘vcfGzFile’ may be used uninitialized [-Wmaybe-uninitialized]
17 | while (gzgets(file, buffer, sizeof(buffer)) != Z_NULL) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcf_parser_fast.cpp: In function ‘bool vcf_genotypes_to_fbm(std::string, Rcpp::Environment, Rcpp::IntegerVector&, int, int)’:
vcf_parser_fast.cpp:278:10: note: ‘vcfGzFile’ was declared here
278 | gzFile vcfGzFile;
| ^~~~~~~~~
In function ‘bool gz_getline(gzFile, std::string&)’,
inlined from ‘Rcpp::List vcf_loci_table(std::string)’ at vcf_parser_fast.cpp:118:27:
vcf_parser_fast.cpp:17:16: warning: ‘vcfGzFile’ may be used uninitialized [-Wmaybe-uninitialized]
17 | while (gzgets(file, buffer, sizeof(buffer)) != Z_NULL) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcf_parser_fast.cpp: In function ‘Rcpp::List vcf_loci_table(std::string)’:
vcf_parser_fast.cpp:74:10: note: ‘vcfGzFile’ was declared here
74 | gzFile vcfGzFile;
| ^~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c write_to_FBM.cpp -o write_to_FBM.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -lz -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpVmaovi/R.INSTALL1f4887104e61e1/tidypopgen/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpVmaovi/R.INSTALL1f4887104e61e1/tidypopgen/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpVmaovi/R.INSTALL1f4887104e61e1/tidypopgen/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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
converting help for package ‘tidypopgen’
finding HTML links ... done
arrange.gen_tbl html
arrange.grouped_gen_tbl html
augment.gt_dapc html
augment_gt_pca html
augment_loci html
augment_loci_gt_pca html
augment_q_matrix html
autoplot.qc_report_indiv html
autoplot.qc_report_loci html
autoplot_gt_admix html
autoplot_gt_cluster_pca html
autoplot_gt_dapc html
autoplot_gt_pca html
autoplot_gt_pcadapt html
autoplot_q_matrix html
c.gt_admix html
cash-set-.gen_tbl html
cbind.gen_tbl html
count_loci html
distruct_colours html
filter.gen_tbl html
filter.grouped_gen_tbl html
filter_high_relatedness html
find_duplicated_loci html
gen_tibble html
get_p_matrix html
get_q_matrix html
gt_add_sf html
gt_admix_reorder_q html
gt_admixture html
gt_as_genind html
gt_as_genlight html
gt_as_geno_lea html
gt_as_hierfstat html
gt_as_plink html
gt_as_vcf html
gt_cluster_pca html
gt_cluster_pca_best_k html
gt_dapc html
gt_extract_f2 html
gt_get_file_names html
gt_has_imputed html
gt_impute_simple html
gt_impute_xgboost html
gt_load html
gt_order_loci html
gt_pca html
gt_pca_autoSVD html
gt_pca_partialSVD html
gt_pca_randomSVD html
gt_pcadapt html
gt_pseudohaploid html
gt_save html
gt_set_imputed html
gt_snmf html
gt_update_backingfile html
gt_uses_imputed html
indiv_het_obs html
indiv_inbreeding html
indiv_missingness html
indiv_ploidy html
is_loci_table_ordered html
load_example_gt html
loci_alt_freq html
loci_chromosomes html
loci_hwe html
loci_ld_clump html
loci_missingness html
loci_names html
loci_pi html
loci_transitions html
loci_transversions html
mutate.gen_tbl html
mutate.grouped_gen_tbl html
nwise_pop_pbs html
pairwise_allele_sharing html
pairwise_grm html
pairwise_ibs html
pairwise_king html
pairwise_pop_fst html
pipe html
pop_fis html
pop_fst html
pop_global_stats html
pop_het_exp html
pop_het_obs html
pop_tajimas_d html
predict_gt_pca html
q_matrix html
qc_report_indiv html
qc_report_loci html
rbind.gen_tbl html
rbind_dry_run html
read_q_files html
reexports html
scale_fill_distruct html
select_loci html
select_loci_if html
show_genotypes html
show_loci html
show_ploidy html
snp_allele_sharing html
snp_ibs html
snp_king html
summary.gt_admix html
summary_rbind_dry_run html
theme_distruct html
tidy.gt_dapc html
tidy.q_matrix html
tidy_gt_pca html
tidypopgen-package html
windows_indiv_roh html
windows_nwise_pop_pbs html
windows_pairwise_pop_fst html
windows_pop_tajimas_d html
windows_stats_generic html
*** 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)