Install log for 'pgenlibr'

* 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++-14 -std=gnu++17 accepts -g... yes
checking for g++-14 -std=gnu++17 option to enable C++11 features... none needed
configure: C++ compiler: g++-14 -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: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpyZJlvY/R.INSTALL1ea4f223f9f19a/pgenlibr/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE     -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++-14 -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 '/home/hornik/tmp/scratch/RtmpyZJlvY/R.INSTALL1ea4f223f9f19a/pgenlibr/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpyZJlvY/R.INSTALL1ea4f223f9f19a/pgenlibr/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpyZJlvY/R.INSTALL1ea4f223f9f19a/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
* DONE (pgenlibr)