* installing *source* package ‘pgenlibr’ ...
** package ‘pgenlibr’ successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... /opt/R/x86_64/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 x86_64 -std=gnu++17 accepts -g... yes
checking for clang++ -arch x86_64 -std=gnu++17 option to enable C++11 features... none needed
configure: C++ compiler: clang++ -arch x86_64 -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 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 -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD   -I.  -Ilibdeflate  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pvar_ffi_support.cpp -o pvar_ffi_support.o
clang++ -arch x86_64 -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-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pgenlib_ffi_support.cpp -o pgenlib_ffi_support.o
clang++ -arch x86_64 -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-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pvar.cpp -o pvar.o
clang++ -arch x86_64 -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-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pgenlibr.cpp -o pgenlibr.o
clang++ -arch x86_64 -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-x86_64/Rlib/4.3/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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD   -I.  -Ilibdeflate  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/zlib_decompress.c -o libdeflate/lib/zlib_decompress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD   -I.  -Ilibdeflate  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/zlib_compress.c -o libdeflate/lib/zlib_compress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD   -I.  -Ilibdeflate  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/utils.c -o libdeflate/lib/utils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD   -I.  -Ilibdeflate  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/gzip_compress.c -o libdeflate/lib/gzip_compress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD   -I.  -Ilibdeflate  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/crc32.c -o libdeflate/lib/crc32.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD   -I.  -Ilibdeflate  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/adler32.c -o libdeflate/lib/adler32.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD   -I.  -Ilibdeflate  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/deflate_decompress.c -o libdeflate/lib/deflate_decompress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD   -I.  -Ilibdeflate  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/deflate_compress.c -o libdeflate/lib/deflate_compress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD   -I.  -Ilibdeflate  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/gzip_decompress.c -o libdeflate/lib/gzip_decompress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD   -I.  -Ilibdeflate  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_ZSTD   -I.  -Ilibdeflate  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/x86/x86_cpu_features.c -o libdeflate/lib/x86/x86_cpu_features.o
clang++ -arch x86_64 -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-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c include/plink2_base.cc -o include/plink2_base.o
clang++ -arch x86_64 -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-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c include/plink2_bits.cc -o include/plink2_bits.o
clang++ -arch x86_64 -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-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c include/pgenlib_misc.cc -o include/pgenlib_misc.o
clang++ -arch x86_64 -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-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c include/pgenlib_read.cc -o include/pgenlib_read.o
clang++ -arch x86_64 -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-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c include/plink2_bgzf.cc -o include/plink2_bgzf.o
clang++ -arch x86_64 -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-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c include/plink2_string.cc -o include/plink2_string.o
clang++ -arch x86_64 -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-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c include/plink2_text.cc -o include/plink2_text.o
clang++ -arch x86_64 -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-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c include/plink2_thread.cc -o include/plink2_thread.o
clang++ -arch x86_64 -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-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c include/plink2_zstfile.cc -o include/plink2_zstfile.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
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libPGDEFLATE.a(arm_cpu_features.o) has no symbols
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 x86_64 -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/x86_64/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-x86_64/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)