* using log directory 'd:/Rcompile/CRANpkg/local/4.5/pgenlibr.Rcheck'
* using R Under development (unstable) (2024-04-30 r86503 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'pgenlibr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pgenlibr' version '0.3.5'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'pgenlibr' can be installed ... ERROR
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/pgenlibr.Rcheck/00install.out' for details.
* DONE
The installation logfile:
* installing *source* package 'pgenlibr' ...
** package 'pgenlibr' successfully unpacked and MD5 sums checked
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
using C++ compiler: 'g++.exe (GCC) 13.2.0'
make[1]: Entering directory '/d/temp/RtmpSq1eZo/R.INSTALL22fb071c06ed2/pgenlibr/src'
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pgenlib_ffi_support.cpp -o pgenlib_ffi_support.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pgenlibr.cpp -o pgenlibr.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pvar.cpp -o pvar.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pvar_ffi_support.cpp -o pvar_ffi_support.o
gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c libdeflate/lib/zlib_decompress.c -o libdeflate/lib/zlib_decompress.o
gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c libdeflate/lib/zlib_compress.c -o libdeflate/lib/zlib_compress.o
gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c libdeflate/lib/utils.c -o libdeflate/lib/utils.o
gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c libdeflate/lib/gzip_compress.c -o libdeflate/lib/gzip_compress.o
gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c libdeflate/lib/crc32.c -o libdeflate/lib/crc32.o
gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c libdeflate/lib/adler32.c -o libdeflate/lib/adler32.o
gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c libdeflate/lib/deflate_decompress.c -o libdeflate/lib/deflate_decompress.o
gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c libdeflate/lib/deflate_compress.c -o libdeflate/lib/deflate_compress.o
gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c libdeflate/lib/gzip_decompress.c -o libdeflate/lib/gzip_decompress.o
gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c libdeflate/lib/arm/arm_cpu_features.c -o libdeflate/lib/arm/arm_cpu_features.o
gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c libdeflate/lib/x86/x86_cpu_features.c -o libdeflate/lib/x86/x86_cpu_features.o
ar rcs libPGDEFLATE.a libdeflate/lib/zlib_decompress.o libdeflate/lib/zlib_compress.o libdeflate/lib/utils.o libdeflate/lib/gzip_compress.o libdeflate/lib/crc32.o libdeflate/lib/adler32.o libdeflate/lib/deflate_decompress.o libdeflate/lib/deflate_compress.o libdeflate/lib/gzip_decompress.o libdeflate/lib/arm/arm_cpu_features.o libdeflate/lib/x86/x86_cpu_features.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c include/plink2_base.cc -o include/plink2_base.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c include/plink2_bits.cc -o include/plink2_bits.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c include/pgenlib_misc.cc -o include/pgenlib_misc.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c include/pgenlib_read.cc -o include/pgenlib_read.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c include/plink2_bgzf.cc -o include/plink2_bgzf.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c include/plink2_string.cc -o include/plink2_string.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c include/plink2_text.cc -o include/plink2_text.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c include/plink2_thread.cc -o include/plink2_thread.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I. -Ilibdeflate -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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++ -std=gnu++17 -shared -s -static-libgcc -o pgenlibr.dll tmp.def RcppExports.o pgenlib_ffi_support.o pgenlibr.o pvar.o pvar_ffi_support.o -L. -lPGDEFLATE -lPLINK2 -lz -lpthread -lzstd -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: ./libPLINK2.a(plink2_text.o):plink2_text.cc:(.text+0x60a): undefined reference to `libdeflate_alloc_decompressor'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: ./libPLINK2.a(plink2_text.o):plink2_text.cc:(.text+0x1b5c): undefined reference to `libdeflate_deflate_decompress'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: ./libPLINK2.a(plink2_text.o):plink2_text.cc:(.text+0x1ecc): undefined reference to `libdeflate_free_decompressor'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: ./libPLINK2.a(plink2_bgzf.o):plink2_bgzf.cc:(.text+0x10c): undefined reference to `libdeflate_deflate_compress'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: ./libPLINK2.a(plink2_bgzf.o):plink2_bgzf.cc:(.text+0x11c): undefined reference to `libdeflate_crc32'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: ./libPLINK2.a(plink2_bgzf.o):plink2_bgzf.cc:(.text+0x528): undefined reference to `libdeflate_deflate_decompress'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: ./libPLINK2.a(plink2_bgzf.o):plink2_bgzf.cc:(.text+0x59b): undefined reference to `libdeflate_deflate_decompress'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: ./libPLINK2.a(plink2_bgzf.o):plink2_bgzf.cc:(.text+0xca9): undefined reference to `libdeflate_alloc_decompressor'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: ./libPLINK2.a(plink2_bgzf.o):plink2_bgzf.cc:(.text+0xedf): undefined reference to `libdeflate_free_decompressor'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: ./libPLINK2.a(plink2_bgzf.o):plink2_bgzf.cc:(.text+0x1239): undefined reference to `libdeflate_free_decompressor'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: ./libPLINK2.a(plink2_bgzf.o):plink2_bgzf.cc:(.text+0x15e6): undefined reference to `libdeflate_alloc_compressor'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: ./libPLINK2.a(plink2_bgzf.o):plink2_bgzf.cc:(.text+0x19be): undefined reference to `libdeflate_free_compressor'
collect2.exe: error: ld returned 1 exit status
make[1]: Leaving directory '/d/temp/RtmpSq1eZo/R.INSTALL22fb071c06ed2/pgenlibr/src'
make[1]: Entering directory '/d/temp/RtmpSq1eZo/R.INSTALL22fb071c06ed2/pgenlibr/src'
make[1]: Leaving directory '/d/temp/RtmpSq1eZo/R.INSTALL22fb071c06ed2/pgenlibr/src'
no DLL was created
ERROR: compilation failed for package 'pgenlibr'
* removing 'd:/Rcompile/CRANpkg/lib/4.5/pgenlibr'
* restoring previous 'd:/Rcompile/CRANpkg/lib/4.5/pgenlibr'