Install log for 'pgenlibr'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/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 g++-13 -std=gnu++17 accepts -g... yes
checking for g++-13 -std=gnu++17 option to enable C++11 features... none needed
configure: C++ compiler: g++-13 -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: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpqlG4Fo/R.INSTALL10d4924e07d9fb/pgenlibr/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pvar_ffi_support.cpp -o pvar_ffi_support.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pgenlib_ffi_support.cpp -o pgenlib_ffi_support.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pvar.cpp -o pvar.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pgenlibr.cpp -o pgenlibr.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c include/plink2_base.cc -o include/plink2_base.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c include/plink2_bits.cc -o include/plink2_bits.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c include/pgenlib_misc.cc -o include/pgenlib_misc.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c include/pgenlib_read.cc -o include/pgenlib_read.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c include/plink2_bgzf.cc -o include/plink2_bgzf.o
include/plink2_bgzf.cc:853:1: warning: embedding a directive within macro arguments is not portable
  853 | #  ifdef __cplusplus
      | ^
include/plink2_bgzf.cc:855:1: warning: embedding a directive within macro arguments is not portable
  855 | #  else
      | ^
include/plink2_bgzf.cc:857:1: warning: embedding a directive within macro arguments is not portable
  857 | #  endif
      | ^
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c include/plink2_string.cc -o include/plink2_string.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c include/plink2_text.cc -o include/plink2_text.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c include/plink2_thread.cc -o include/plink2_thread.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT    -I.    -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -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
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/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-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpqlG4Fo/R.INSTALL10d4924e07d9fb/pgenlibr/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpqlG4Fo/R.INSTALL10d4924e07d9fb/pgenlibr/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpqlG4Fo/R.INSTALL10d4924e07d9fb/pgenlibr/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/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
* creating tarball
packaged installation of ‘pgenlibr’ as ‘pgenlibr_0.3.5_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (pgenlibr)