* installing *source* package ‘DEploid’ ... ** package ‘DEploid’ 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 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'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c rvcf.cpp -o rvcf.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c dEploidr.cpp -o dEploidr.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c test_exports.cpp -o test_exports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/dEploidIO.cpp -o DEploid/dEploidIO.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/ibd.cpp -o DEploid/ibd.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/mcmc.cpp -o DEploid/mcmc.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/panel.cpp -o DEploid/panel.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/txtReader.cpp -o DEploid/txtReader.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/updateHap.cpp -o DEploid/updateHap.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/utility.cpp -o DEploid/utility.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/variantIndex.cpp -o DEploid/variantIndex.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/vcfReader.cpp -o DEploid/vcfReader.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/gzstream/gzstream.cpp -o DEploid/gzstream/gzstream.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/random/fastfunc.cpp -o DEploid/random/fastfunc.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/random/random_generator.cpp -o DEploid/random/random_generator.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/random/mersenne_twister.cpp -o DEploid/random/mersenne_twister.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/export/dEploidIOExportPosteriorProb.cpp -o DEploid/export/dEploidIOExportPosteriorProb.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/export/writeMcmcRelated.cpp -o DEploid/export/writeMcmcRelated.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/lasso/dEploidLasso.cpp -o DEploid/lasso/dEploidLasso.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/lasso/lasso.cpp -o DEploid/lasso/lasso.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/lasso/lassoDBG.cpp -o DEploid/lasso/lassoDBG.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/debug/vcfReaderDebug.cpp -o DEploid/debug/vcfReaderDebug.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fPIC -falign-functions=64 -Wall -g -O2 -c DEploid/debug/mcmcDebug.cpp -o DEploid/debug/mcmcDebug.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 DEploid.so rvcf.o dEploidr.o test_exports.o RcppExports.o init.o DEploid/dEploidIO.o DEploid/ibd.o DEploid/mcmc.o DEploid/panel.o DEploid/txtReader.o DEploid/updateHap.o DEploid/utility.o DEploid/variantIndex.o DEploid/vcfReader.o DEploid/gzstream/gzstream.o DEploid/random/fastfunc.o DEploid/random/random_generator.o DEploid/random/mersenne_twister.o DEploid/export/dEploidIOExportPosteriorProb.o DEploid/export/writeMcmcRelated.o DEploid/lasso/dEploidLasso.o DEploid/lasso/lasso.o DEploid/lasso/lassoDBG.o DEploid/debug/vcfReaderDebug.o DEploid/debug/mcmcDebug.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Volumes/Builds/packages/big-sur-arm64/results/4.3/DEploid.Rcheck/00LOCK-DEploid/00new/DEploid/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 (DEploid)