* 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) 12.3.0'
make[1]: Entering directory '/d/temp/2025_02_03_01_50_00_1639/Rtmp2hy8zV/R.INSTALL2ec9838598c/pgenlibr/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/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-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/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-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pvar.cpp -o pvar.o
gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/libdeflate/lib/zlib_decompress.c -o ../inst/include/libdeflate/lib/zlib_decompress.o
gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/libdeflate/lib/zlib_compress.c -o ../inst/include/libdeflate/lib/zlib_compress.o
gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/libdeflate/lib/utils.c -o ../inst/include/libdeflate/lib/utils.o
gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/libdeflate/lib/gzip_compress.c -o ../inst/include/libdeflate/lib/gzip_compress.o
gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/libdeflate/lib/crc32.c -o ../inst/include/libdeflate/lib/crc32.o
gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/libdeflate/lib/adler32.c -o ../inst/include/libdeflate/lib/adler32.o
gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/libdeflate/lib/deflate_decompress.c -o ../inst/include/libdeflate/lib/deflate_decompress.o
gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/libdeflate/lib/deflate_compress.c -o ../inst/include/libdeflate/lib/deflate_compress.o
gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/libdeflate/lib/gzip_decompress.c -o ../inst/include/libdeflate/lib/gzip_decompress.o
gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/libdeflate/lib/arm/arm_cpu_features.c -o ../inst/include/libdeflate/lib/arm/arm_cpu_features.o
gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/libdeflate/lib/x86/x86_cpu_features.c -o ../inst/include/libdeflate/lib/x86/x86_cpu_features.o
ar rcs libPGDEFLATE.a ../inst/include/libdeflate/lib/zlib_decompress.o ../inst/include/libdeflate/lib/zlib_compress.o ../inst/include/libdeflate/lib/utils.o ../inst/include/libdeflate/lib/gzip_compress.o ../inst/include/libdeflate/lib/crc32.o ../inst/include/libdeflate/lib/adler32.o ../inst/include/libdeflate/lib/deflate_decompress.o ../inst/include/libdeflate/lib/deflate_compress.o ../inst/include/libdeflate/lib/gzip_decompress.o ../inst/include/libdeflate/lib/arm/arm_cpu_features.o ../inst/include/libdeflate/lib/x86/x86_cpu_features.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/include/plink2_base.cc -o ../inst/include/include/plink2_base.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/include/plink2_bits.cc -o ../inst/include/include/plink2_bits.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/include/pgenlib_ffi_support.cc -o ../inst/include/include/pgenlib_ffi_support.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/include/pgenlib_misc.cc -o ../inst/include/include/pgenlib_misc.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/include/pgenlib_read.cc -o ../inst/include/include/pgenlib_read.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/include/plink2_bgzf.cc -o ../inst/include/include/plink2_bgzf.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/include/plink2_htable.cc -o ../inst/include/include/plink2_htable.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/include/plink2_memory.cc -o ../inst/include/include/plink2_memory.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/include/plink2_string.cc -o ../inst/include/include/plink2_string.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/include/plink2_text.cc -o ../inst/include/include/plink2_text.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/include/plink2_thread.cc -o ../inst/include/include/plink2_thread.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/include/plink2_zstfile.cc -o ../inst/include/include/plink2_zstfile.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ../inst/include/include/pvar_ffi_support.cc -o ../inst/include/include/pvar_ffi_support.o
../inst/include/include/pvar_ffi_support.cc: In function 'plink2::PglErr plink2::LoadMinimalPvarEx(const char*, LoadMinimalPvarFlags, MinimalPvar*, char*)':
../inst/include/include/pvar_ffi_support.cc:426:38: warning: 'variant_bps' may be used uninitialized [-Wmaybe-uninitialized]
426 | if (unlikely(ScanIntAbsDefcap(token_ptrs[kPvarColPos], &(variant_bps[variant_idx])))) {
| ^
../inst/include/include/pvar_ffi_support.cc:349:14: note: 'variant_bps' was declared here
349 | int32_t* variant_bps;
| ^~~~~~~~~~~
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
g++ -std=gnu++17 -shared -s -static-libgcc -o pgenlibr.dll tmp.def RcppExports.o pgenlibr.o pvar.o -L. -lPLINK2 -lzstd -lPGDEFLATE -lz -lpthread -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.3.3/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2025_02_03_01_50_00_1639/Rtmp2hy8zV/R.INSTALL2ec9838598c/pgenlibr/src'
make[1]: Entering directory '/d/temp/2025_02_03_01_50_00_1639/Rtmp2hy8zV/R.INSTALL2ec9838598c/pgenlibr/src'
make[1]: Leaving directory '/d/temp/2025_02_03_01_50_00_1639/Rtmp2hy8zV/R.INSTALL2ec9838598c/pgenlibr/src'
installing to d:/Rcompile/CRANpkg/lib/4.3/00LOCK-pgenlibr/00new/pgenlibr/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'pgenlibr' as pgenlibr_0.4.0.zip
* DONE (pgenlibr)