* installing *source* package ‘pgenlibr’ ... ** this is package ‘pgenlibr’ version ‘0.4.0’ ** 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 1.5.5 library detected -- skipping zstd compilation configure: libdeflate 1.23 library detected -- skipping libdeflate compilation 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 -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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 -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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 -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ../inst/include/include/plink2_base.cc -o ../inst/include/include/plink2_base.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ../inst/include/include/plink2_bits.cc -o ../inst/include/include/plink2_bits.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ../inst/include/include/pgenlib_ffi_support.cc -o ../inst/include/include/pgenlib_ffi_support.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ../inst/include/include/pgenlib_misc.cc -o ../inst/include/include/pgenlib_misc.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ../inst/include/include/pgenlib_read.cc -o ../inst/include/include/pgenlib_read.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ../inst/include/include/plink2_bgzf.cc -o ../inst/include/include/plink2_bgzf.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ../inst/include/include/plink2_htable.cc -o ../inst/include/include/plink2_htable.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ../inst/include/include/plink2_memory.cc -o ../inst/include/include/plink2_memory.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ../inst/include/include/plink2_string.cc -o ../inst/include/include/plink2_string.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ../inst/include/include/plink2_text.cc -o ../inst/include/include/plink2_text.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ../inst/include/include/plink2_thread.cc -o ../inst/include/include/plink2_thread.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ../inst/include/include/plink2_zstfile.cc -o ../inst/include/include/plink2_zstfile.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I../inst/include -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ../inst/include/include/pvar_ffi_support.cc -o ../inst/include/include/pvar_ffi_support.o ar rcs libPLINK2.a ../inst/include/include/plink2_base.o ../inst/include/include/plink2_bits.o ../inst/include/include/pgenlib_ffi_support.o ../inst/include/include/pgenlib_misc.o ../inst/include/include/pgenlib_read.o ../inst/include/include/plink2_bgzf.o ../inst/include/include/plink2_htable.o ../inst/include/include/plink2_memory.o ../inst/include/include/plink2_string.o ../inst/include/include/plink2_text.o ../inst/include/include/plink2_thread.o ../inst/include/include/plink2_zstfile.o ../inst/include/include/pvar_ffi_support.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 pgenlibr.so pvar.o pgenlibr.o RcppExports.o -lPLINK2 -L. -L/opt/R/x86_64/lib -lzstd -pthread -L/opt/R/x86_64/lib -ldeflate -lz -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.5/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)