* 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++.exe (GCC) 14.2.0'
make[1]: Entering directory '/d/temp/2025_08_28_01_50_00_14304/Rtmpc5BvXz/R.INSTALL3984552a2d2c/tidypopgen/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alt_freq_dip_pseudo_cpp.cpp -o alt_freq_dip_pseudo_cpp.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c compute_np_mn.cpp -o compute_np_mn.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fbm_prod_and_rowSumSq.cpp -o fbm_prod_and_rowSumSq.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c grouped_alt_freq_dip_pseudo_cpp.cpp -o grouped_alt_freq_dip_pseudo_cpp.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c grouped_missingness_cpp.cpp -o grouped_missingness_cpp.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c grouped_summaries_dip_pseudo_cpp.cpp -o grouped_summaries_dip_pseudo_cpp.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gt_grouped_pi_diploid.cpp -o gt_grouped_pi_diploid.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gt_ind_hetero.cpp -o gt_ind_hetero.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gt_pi_diploid.cpp -o gt_pi_diploid.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hwe.cpp -o hwe.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pairwise_fst_hudson_loop.cpp -o pairwise_fst_hudson_loop.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pairwise_fst_nei87_loop.cpp -o pairwise_fst_nei87_loop.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pairwise_fst_wc84_loop.cpp -o pairwise_fst_wc84_loop.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_packedancestry.cpp -o read_packedancestry.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c snp_as.cpp -o snp_as.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c snp_ibs.cpp -o snp_ibs.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c snp_king.cpp -o snp_king.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.5/rmio/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c write_to_FBM.cpp -o write_to_FBM.o
g++ -std=gnu++17 -shared -s -static-libgcc -o tidypopgen.dll tmp.def 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 -lz -fopenmp -LD:/RCompile/recent/R-4.5.1/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.5.1/bin/x64 -lRblas -lgfortran -lquadmath -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.5.1/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2025_08_28_01_50_00_14304/Rtmpc5BvXz/R.INSTALL3984552a2d2c/tidypopgen/src'
make[1]: Entering directory '/d/temp/2025_08_28_01_50_00_14304/Rtmpc5BvXz/R.INSTALL3984552a2d2c/tidypopgen/src'
make[1]: Leaving directory '/d/temp/2025_08_28_01_50_00_14304/Rtmpc5BvXz/R.INSTALL3984552a2d2c/tidypopgen/src'
installing to d:/Rcompile/CRANpkg/lib/4.5/00LOCK-tidypopgen/00new/tidypopgen/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'tidypopgen' as tidypopgen_0.3.2.zip
* DONE (tidypopgen)