* installing *source* package 'pgenlibr' ... ** this is package 'pgenlibr' version '0.4.0' ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs using C++ compiler: 'g++.exe (GCC) 13.3.0' g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c pgenlibr.cpp -o pgenlibr.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c pvar.cpp -o pvar.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/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/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/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/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/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/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/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/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/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/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/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/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/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/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/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/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/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/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/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/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/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/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c ../inst/include/include/plink2_base.cc -o ../inst/include/include/plink2_base.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c ../inst/include/include/plink2_bits.cc -o ../inst/include/include/plink2_bits.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -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/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c ../inst/include/include/pgenlib_misc.cc -o ../inst/include/include/pgenlib_misc.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c ../inst/include/include/pgenlib_read.cc -o ../inst/include/include/pgenlib_read.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c ../inst/include/include/plink2_bgzf.cc -o ../inst/include/include/plink2_bgzf.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c ../inst/include/include/plink2_htable.cc -o ../inst/include/include/plink2_htable.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c ../inst/include/include/plink2_memory.cc -o ../inst/include/include/plink2_memory.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c ../inst/include/include/plink2_string.cc -o ../inst/include/include/plink2_string.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c ../inst/include/include/plink2_text.cc -o ../inst/include/include/plink2_text.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c ../inst/include/include/plink2_thread.cc -o ../inst/include/include/plink2_thread.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c ../inst/include/include/plink2_zstfile.cc -o ../inst/include/include/plink2_zstfile.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DNO_UNALIGNED -DLIBDEFLATE_STATIC -DPGENLIB_NOPRINT -I../inst/include -I../inst/include/libdeflate -I'D:/RCompile/CRANincoming/R-devel/lib/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c ../inst/include/include/pvar_ffi_support.cc -o ../inst/include/include/pvar_ffi_support.o In file included from ../inst/include/include/plink2_bits.h:23, from ../inst/include/include/pgenlib_misc.h:77, from ../inst/include/include/pvar_ffi_support.h:20, from ../inst/include/include/pvar_ffi_support.cc:17: ../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/plink2_base.h:275:46: note: in definition of macro 'unlikely' 275 | # define unlikely(expr) __builtin_expect(!!(expr), 0) | ^~~~ ../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:/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 installing to d:/RCompile/CRANincoming/R-devel/lib/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 * DONE (pgenlibr)