Install log for 'milorGWAS'

* installing *source* package ‘milorGWAS’ ...
** package ‘milorGWAS’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c chr_convert.cpp -o chr_convert.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c dosage_files.cpp -o dosage_files.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c genotype_probas.cpp -o genotype_probas.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gwas_approx_pql_bed.cpp -o gwas_approx_pql_bed.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gwas_approx_pql_dosages.cpp -o gwas_approx_pql_dosages.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gwas_logit_offset_bed.cpp -o gwas_logit_offset_bed.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gwas_logit_offset_dosages.cpp -o gwas_logit_offset_dosages.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c manhattan_thinning.cpp -o manhattan_thinning.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c matrix-varia.cpp -o matrix-varia.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c matrix4.cpp -o matrix4.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c read_dose_file.cpp -o read_dose_file.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c read_vcf_header.cpp -o read_vcf_header.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c snp_filter.cpp -o snp_filter.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../inst/include/milorGWAS/  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/gaston/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c token.cpp -o token.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o milorGWAS.so RcppExports.o chr_convert.o dosage_files.o genotype_probas.o gwas_approx_pql_bed.o gwas_approx_pql_dosages.o gwas_logit_offset_bed.o gwas_logit_offset_dosages.o manhattan_thinning.o matrix-varia.o matrix4.o read_dose_file.o read_vcf_header.o snp_filter.o token.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.4/milorGWAS.Rcheck/00LOCK-milorGWAS/00new/milorGWAS/libs
** generating debug symbols (dSYM)
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (milorGWAS)