* installing to library ‘/home/hornik/tmp/R.check/r-patched-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 13.2.0-24) 13.2.0’
make[1]: Entering directory '/tmp/Rtmp8BGUmO/R.INSTALL20ce46596879f1/pgenlibr/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -I. -I'/home/hornik/tmp/R.check/r-patched-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-patched-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-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp8BGUmO/R.INSTALL20ce46596879f1/pgenlibr/src'
make[1]: Entering directory '/tmp/Rtmp8BGUmO/R.INSTALL20ce46596879f1/pgenlibr/src'
make[1]: Leaving directory '/tmp/Rtmp8BGUmO/R.INSTALL20ce46596879f1/pgenlibr/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-pgenlibr/00new/pgenlibr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘pgenlibr’
finding HTML links ... done
AlleleCodeBuf html
BoolBuf html
Buf html
ClosePgen html
ClosePvar html
GetAlleleCode html
GetAlleleCt html
GetMaxAlleleCt html
GetRawSampleCt html
GetVariantCt html
GetVariantId html
GetVariantsById html
HardcallPhasePresent html
IntAlleleCodeBuf html
IntBuf html
NewPgen html
NewPvar html
Read html
ReadAlleles html
ReadHardcalls html
ReadIntList html
ReadList html
VariantScores html
pgenlibr-package html
** 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)