* installing *source* package ‘pgenlibr’ ... ** this is package ‘pgenlibr’ version ‘0.5.6’ ** 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 g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 accepts -g... yes checking for g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 option to enable C++11 features... -std=gnu++11 configure: C++ compiler: g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 configure: zstd 1.5.7 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: ‘g++-15 (Debian 15.2.0-14) 15.2.0’ g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c pvar.cpp -o pvar.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c pgenlibr.cpp -o pgenlibr.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c RcppExports.cpp -o RcppExports.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c ../inst/include/include/plink2_base.cc -o ../inst/include/include/plink2_base.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c ../inst/include/include/plink2_bits.cc -o ../inst/include/include/plink2_bits.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c ../inst/include/include/pgenlib_ffi_support.cc -o ../inst/include/include/pgenlib_ffi_support.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c ../inst/include/include/pgenlib_misc.cc -o ../inst/include/include/pgenlib_misc.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c ../inst/include/include/pgenlib_read.cc -o ../inst/include/include/pgenlib_read.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c ../inst/include/include/plink2_bgzf.cc -o ../inst/include/include/plink2_bgzf.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c ../inst/include/include/plink2_float.cc -o ../inst/include/include/plink2_float.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c ../inst/include/include/plink2_htable.cc -o ../inst/include/include/plink2_htable.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c ../inst/include/include/plink2_memory.cc -o ../inst/include/include/plink2_memory.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c ../inst/include/include/plink2_string.cc -o ../inst/include/include/plink2_string.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c ../inst/include/include/plink2_text.cc -o ../inst/include/include/plink2_text.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c ../inst/include/include/plink2_thread.cc -o ../inst/include/include/plink2_thread.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -c ../inst/include/include/plink2_zstfile.cc -o ../inst/include/include/plink2_zstfile.o g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-xtra/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/hornik/tmp/CRAN_special_gcc-san/Library/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-stringop-truncation -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_float.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 g++-15 -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-xtra/lib -Wl,-O1 -o pgenlibr.so pvar.o pgenlibr.o RcppExports.o -lPLINK2 -L. -lzstd -ldeflate -lz -lpthread -L/home/hornik/tmp/R-d-gcc-xtra/lib -lR installing to /home/hornik/tmp/CRAN_special_gcc-san/pgenlibr.Rcheck/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)