* installing *source* package ‘pgenlibr’ ... ** package ‘pgenlibr’ successfully unpacked and MD5 sums checked ** using staged installation checking for pkg-config... /opt/R/arm64/bin/pkg-config checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether clang++ -arch arm64 -std=gnu++17 accepts -g... yes checking for clang++ -arch arm64 -std=gnu++17 option to enable C++11 features... none needed configure: C++ compiler: clang++ -arch arm64 -std=gnu++17 configure: zstd not detected by pkg-config; falling back on system header file check yes configure: libdeflate not detected by pkg-config; falling back on system header file check no configure: simde not detected by pkg-config; falling back on system header file check no configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘Apple clang version 13.0.0 (clang-1300.0.29.30)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 pvar_ffi_support.cpp -o pvar_ffi_support.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 pgenlib_ffi_support.cpp -o pgenlib_ffi_support.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 pvar.cpp -o pvar.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 pgenlibr.cpp -o pgenlibr.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 RcppExports.cpp -o RcppExports.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 libdeflate/lib/zlib_decompress.c -o libdeflate/lib/zlib_decompress.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 libdeflate/lib/zlib_compress.c -o libdeflate/lib/zlib_compress.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 libdeflate/lib/utils.c -o libdeflate/lib/utils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 libdeflate/lib/gzip_compress.c -o libdeflate/lib/gzip_compress.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 libdeflate/lib/crc32.c -o libdeflate/lib/crc32.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 libdeflate/lib/adler32.c -o libdeflate/lib/adler32.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 libdeflate/lib/deflate_decompress.c -o libdeflate/lib/deflate_decompress.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 libdeflate/lib/deflate_compress.c -o libdeflate/lib/deflate_compress.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 libdeflate/lib/gzip_decompress.c -o libdeflate/lib/gzip_decompress.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 libdeflate/lib/arm/arm_cpu_features.c -o libdeflate/lib/arm/arm_cpu_features.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 libdeflate/lib/x86/x86_cpu_features.c -o libdeflate/lib/x86/x86_cpu_features.o ar rcs libPGDEFLATE.a libdeflate/lib/zlib_decompress.o libdeflate/lib/zlib_compress.o libdeflate/lib/utils.o libdeflate/lib/gzip_compress.o libdeflate/lib/crc32.o libdeflate/lib/adler32.o libdeflate/lib/deflate_decompress.o libdeflate/lib/deflate_compress.o libdeflate/lib/gzip_decompress.o libdeflate/lib/arm/arm_cpu_features.o libdeflate/lib/x86/x86_cpu_features.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 include/plink2_base.cc -o include/plink2_base.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 include/plink2_bits.cc -o include/plink2_bits.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 include/pgenlib_misc.cc -o include/pgenlib_misc.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 include/pgenlib_read.cc -o include/pgenlib_read.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 include/plink2_bgzf.cc -o include/plink2_bgzf.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 include/plink2_string.cc -o include/plink2_string.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 include/plink2_text.cc -o include/plink2_text.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 include/plink2_thread.cc -o include/plink2_thread.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD -I. -Ilibdeflate -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 include/plink2_zstfile.cc -o include/plink2_zstfile.o ar rcs libPLINK2.a include/plink2_base.o include/plink2_bits.o include/pgenlib_misc.o include/pgenlib_read.o include/plink2_bgzf.o include/plink2_string.o include/plink2_text.o include/plink2_thread.o include/plink2_zstfile.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o pgenlibr.so pvar_ffi_support.o pgenlib_ffi_support.o pvar.o pgenlibr.o RcppExports.o -lPLINK2 -L. -lzstd -lPGDEFLATE -lz -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Volumes/Builds/packages/big-sur-arm64/results/4.3/pgenlibr.Rcheck/00LOCK-pgenlibr/00new/pgenlibr/libs ** generating debug symbols (dSYM) ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (pgenlibr)