* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’ * installing *source* package ‘pgenlibr’ ... ** package ‘pgenlibr’ successfully unpacked and MD5 sums checked ** using staged installation checking for pkg-config... /usr/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++-18 -std=gnu++17 accepts -g... yes checking for clang++-18 -std=gnu++17 option to enable C++11 features... none needed configure: C++ compiler: clang++-18 -std=gnu++17 configure: zstd 1.5.5 library detected -- skipping zstd compilation configure: libdeflate 1.20 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: ‘Debian clang version 18.1.4 (1)’ make[1]: Entering directory '/tmp/RtmpQv0XDf/R.INSTALL70899137982e9/pgenlibr/src' clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pvar_ffi_support.cpp -o pvar_ffi_support.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pgenlib_ffi_support.cpp -o pgenlib_ffi_support.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pvar.cpp -o pvar.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pgenlibr.cpp -o pgenlibr.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c include/plink2_base.cc -o include/plink2_base.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c include/plink2_bits.cc -o include/plink2_bits.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c include/pgenlib_misc.cc -o include/pgenlib_misc.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c include/pgenlib_read.cc -o include/pgenlib_read.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c include/plink2_bgzf.cc -o include/plink2_bgzf.o include/plink2_bgzf.cc:853:4: warning: embedding a directive within macro arguments has undefined behavior [-Wembedded-directive] 853 | # ifdef __cplusplus | ^ include/plink2_bgzf.cc:855:4: warning: embedding a directive within macro arguments has undefined behavior [-Wembedded-directive] 855 | # else | ^ 2 warnings generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c include/plink2_string.cc -o include/plink2_string.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c include/plink2_text.cc -o include/plink2_text.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c include/plink2_thread.cc -o include/plink2_thread.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -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++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o pgenlibr.so pvar_ffi_support.o pgenlib_ffi_support.o pvar.o pgenlibr.o RcppExports.o -lPLINK2 -L. -lzstd -ldeflate -lz -lpthread -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR make[1]: Leaving directory '/tmp/RtmpQv0XDf/R.INSTALL70899137982e9/pgenlibr/src' make[1]: Entering directory '/tmp/RtmpQv0XDf/R.INSTALL70899137982e9/pgenlibr/src' make[1]: Leaving directory '/tmp/RtmpQv0XDf/R.INSTALL70899137982e9/pgenlibr/src' installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-pgenlibr/00new/pgenlibr/libs ** 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)