* installing *source* package ‘pgenlibr’ ...
** this is package ‘pgenlibr’ version ‘0.4.0’
** 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++-19 -std=gnu++17 accepts -g... yes
checking for clang++-19 -std=gnu++17 option to enable C++11 features... none needed
configure: C++ compiler: clang++-19 -std=gnu++17
configure: zstd 1.5.6 library detected -- skipping zstd compilation
configure: libdeflate 1.22 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 19.1.6 (1+b1)’
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c pvar.cpp -o pvar.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c pgenlibr.cpp -o pgenlibr.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ../inst/include/include/plink2_base.cc -o ../inst/include/include/plink2_base.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ../inst/include/include/plink2_bits.cc -o ../inst/include/include/plink2_bits.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ../inst/include/include/pgenlib_ffi_support.cc -o ../inst/include/include/pgenlib_ffi_support.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ../inst/include/include/pgenlib_misc.cc -o ../inst/include/include/pgenlib_misc.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ../inst/include/include/pgenlib_read.cc -o ../inst/include/include/pgenlib_read.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ../inst/include/include/plink2_bgzf.cc -o ../inst/include/include/plink2_bgzf.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ../inst/include/include/plink2_htable.cc -o ../inst/include/include/plink2_htable.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ../inst/include/include/plink2_memory.cc -o ../inst/include/include/plink2_memory.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ../inst/include/include/plink2_string.cc -o ../inst/include/include/plink2_string.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ../inst/include/include/plink2_text.cc -o ../inst/include/include/plink2_text.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ../inst/include/include/plink2_thread.cc -o ../inst/include/include/plink2_thread.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ../inst/include/include/plink2_zstfile.cc -o ../inst/include/include/plink2_zstfile.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -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++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o pgenlibr.so pvar.o pgenlibr.o RcppExports.o -lPLINK2 -L. -lzstd -ldeflate -lz -lpthread -L/home/hornik/tmp/R/lib -lR
installing to /srv/hornik/tmp/CRAN_pretest/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)