* installing *source* package ‘vcfR’ ... ** package ‘vcfR’ 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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c NM2winNM.cpp -o NM2winNM.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ad_frequency.cpp -o ad_frequency.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c deprecated_funcs.cpp -o deprecated_funcs.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extract_gt.cpp -o extract_gt.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c freq_peak.cpp -o freq_peak.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gt_to_popsum.cpp -o gt_to_popsum.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c is_het.cpp -o is_het.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c masplit.cpp -o masplit.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pair_sort.cpp -o pair_sort.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rank_variants.cpp -o rank_variants.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c read_vcfR.cpp -o read_vcfR.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c seq_to_rects.cpp -o seq_to_rects.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c var_window.cpp -o var_window.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vcfRCommon.cpp -o vcfRCommon.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/4.4/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c write_vcfR.cpp -o write_vcfR.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 vcfR.so NM2winNM.o RcppExports.o ad_frequency.o deprecated_funcs.o extract_gt.o freq_peak.o gt_to_popsum.o is_het.o masplit.o pair_sort.o rank_variants.o read_vcfR.o seq_to_rects.o var_window.o vcfRCommon.o write_vcfR.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.4/vcfR.Rcheck/00LOCK-vcfR/00new/vcfR/libs ** generating debug symbols (dSYM) ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘rbind’ from package ‘base’ in package ‘vcfR’ Creating a generic function for ‘nrow’ from package ‘base’ in package ‘vcfR’ ** help *** installing help indices ** 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 (vcfR)