* installing *source* package 'seqminer' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'g++.exe (GCC) 13.2.0' using C++17 g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BCFReader.cpp -o BCFReader.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BGenFile.cpp -o BGenFile.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BGenIndex.cpp -o BGenIndex.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BGenVariant.cpp -o BGenVariant.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Exception.cpp -o Exception.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FileIO.cpp -o FileIO.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GeneLoader.cpp -o GeneLoader.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MmapFile.cpp -o MmapFile.o MmapFile.cpp:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PatternMatch.cpp -o PatternMatch.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PeopleSet.cpp -o PeopleSet.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PlinkInputFile.cpp -o PlinkInputFile.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PlinkOutputFile.cpp -o PlinkOutputFile.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Profiler.cpp -o Profiler.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_CPP_interface.cpp -o R_CPP_interface.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RangeList.cpp -o RangeList.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Rannotation.cpp -o Rannotation.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SimpleMatrix.cpp -o SimpleMatrix.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SingleChromosomeBCFIndex.cpp -o SingleChromosomeBCFIndex.o SingleChromosomeBCFIndex.cpp:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SingleChromosomeVCFIndex.cpp -o SingleChromosomeVCFIndex.o SingleChromosomeVCFIndex.cpp:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition SingleChromosomeVCFIndex.cpp: In member function 'int SingleChromosomeVCFIndex::createIndex()': SingleChromosomeVCFIndex.cpp:69:15: warning: unused variable 'fn' [-Wunused-variable] 69 | const char* fn = vcfFile_.c_str(); | ^~ SingleChromosomeVCFIndex.cpp: In member function 'int SingleChromosomeVCFIndex::mapIndex()': SingleChromosomeVCFIndex.cpp:201:15: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int64_t' {aka 'long long int'} [-Wsign-compare] 201 | if (Nrecord != d[1]) { | ~~~~~~~~^~~~~~~ SingleChromosomeVCFIndex.cpp: In member function 'int SingleChromosomeVCFIndex::query(int, int, int64_t*)': SingleChromosomeVCFIndex.cpp:253:41: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'double' [-Wformat=] 253 | REprintf("found %d position, e.g. %ld %ld\n", (int)(ub - lb), | ~~^ | | | long int | %f 254 | (double) (*lb).pos, | ~~~~~~~~~~~~~~~~~~ | | | double SingleChromosomeVCFIndex.cpp:253:45: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'double' [-Wformat=] 253 | REprintf("found %d position, e.g. %ld %ld\n", (int)(ub - lb), | ~~^ | | | long int | %f 254 | (double) (*lb).pos, 255 | (double) (*lb).offset); | ~~~~~~~~~~~~~~~~~~~~~ | | | double g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TypeConversion.cpp -o TypeConversion.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Utils.cpp -o Utils.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c VCFHeader.cpp -o VCFHeader.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c VCFIndividual.cpp -o VCFIndividual.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c VCFInfo.cpp -o VCFInfo.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c VCFInputFile.cpp -o VCFInputFile.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c VCFUtil.cpp -o VCFUtil.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bcf.c -o bcf.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bcf_index.c -o bcf_index.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bcfutils.c -o bcfutils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bedidx.c -o bedidx.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bgen2genoLoader.cpp -o bgen2genoLoader.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bgzf.c -o bgzf.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c knetfile.c -o knetfile.o In file included from knetfile.c:45: knetfile.h:17: warning: "R_Realloc" redefined 17 | #define R_Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) ) | In file included from D:/RCompile/recent/R/include/R.h:78, from knetfile.h:15: D:/RCompile/recent/R/include/R_ext/RS.h:65: note: this is the location of the previous definition 65 | #define R_Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (R_SIZE_T)((n) * sizeof(t)) ) | gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kstring.c -o kstring.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c plink2genoLoader.cpp -o plink2genoLoader.o plink2genoLoader.cpp: In function 'int readBedToMatrixByIndex(const std::string&, int, int, const std::vector&, const std::vector&, SEXP)': plink2genoLoader.cpp:126:3: warning: 'snpMajorMode' may be used uninitialized [-Wmaybe-uninitialized] 126 | if (snpMajorMode) { | ^~ plink2genoLoader.cpp:78:8: note: 'snpMajorMode' was declared here 78 | bool snpMajorMode; | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rvMetaLoader.cpp -o rvMetaLoader.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scbcf2genoLoader.cpp -o scbcf2genoLoader.o scbcf2genoLoader.cpp: In function 'int parseBCFVariant(const BCFHeader&, uint32_t, uint32_t, std::vector, std::vector*, std::vector >*)': scbcf2genoLoader.cpp:287:10: warning: unused variable 'format_type' [-Wunused-variable] 287 | int8_t format_type = *pIndv; | ^~~~~~~~~~~ g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scvcf2genoLoader.cpp -o scvcf2genoLoader.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c seqForStat.c -o seqForStat.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c seqminer.c -o seqminer.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c seqminer_init.c -o seqminer_init.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tabixLoader.cpp -o tabixLoader.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tabix_index.c -o tabix_index.o tabix_index.c:19:14: warning: 'currentTime' defined but not used [-Wunused-function] 19 | static char* currentTime(void) { | ^~~~~~~~~~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcf.c -o vcf.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcf2genoLoader.cpp -o vcf2genoLoader.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/common/debug.c -o zstd/lib/common/debug.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/common/entropy_common.c -o zstd/lib/common/entropy_common.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/common/error_private.c -o zstd/lib/common/error_private.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/common/fse_decompress.c -o zstd/lib/common/fse_decompress.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/common/pool.c -o zstd/lib/common/pool.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/common/threading.c -o zstd/lib/common/threading.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/common/xxhash.c -o zstd/lib/common/xxhash.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/common/zstd_common.c -o zstd/lib/common/zstd_common.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/compress/fse_compress.c -o zstd/lib/compress/fse_compress.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/compress/hist.c -o zstd/lib/compress/hist.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/compress/huf_compress.c -o zstd/lib/compress/huf_compress.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/compress/zstd_compress.c -o zstd/lib/compress/zstd_compress.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/compress/zstd_double_fast.c -o zstd/lib/compress/zstd_double_fast.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/compress/zstd_fast.c -o zstd/lib/compress/zstd_fast.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/compress/zstd_lazy.c -o zstd/lib/compress/zstd_lazy.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/compress/zstd_ldm.c -o zstd/lib/compress/zstd_ldm.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/compress/zstd_opt.c -o zstd/lib/compress/zstd_opt.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/compress/zstdmt_compress.c -o zstd/lib/compress/zstdmt_compress.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/decompress/huf_decompress.c -o zstd/lib/decompress/huf_decompress.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/decompress/zstd_decompress.c -o zstd/lib/decompress/zstd_decompress.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/deprecated/zbuff_common.c -o zstd/lib/deprecated/zbuff_common.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/deprecated/zbuff_compress.c -o zstd/lib/deprecated/zbuff_compress.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/deprecated/zbuff_decompress.c -o zstd/lib/deprecated/zbuff_decompress.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/dictBuilder/cover.c -o zstd/lib/dictBuilder/cover.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/dictBuilder/divsufsort.c -o zstd/lib/dictBuilder/divsufsort.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/dictBuilder/fastcover.c -o zstd/lib/dictBuilder/fastcover.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/dictBuilder/zdict.c -o zstd/lib/dictBuilder/zdict.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/legacy/zstd_v05.c -o zstd/lib/legacy/zstd_v05.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/legacy/zstd_v06.c -o zstd/lib/legacy/zstd_v06.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zstd/lib/legacy/zstd_v07.c -o zstd/lib/legacy/zstd_v07.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DSTRICT_R_HEADERS=1 -DNDEBUG -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sqlite/sqlite3.c -o sqlite/sqlite3.o sqlite/sqlite3.c: In function 'sqlite3ThreadJoin': sqlite/sqlite3.c:29184:8: warning: variable 'bRc' set but not used [-Wunused-but-set-variable] 29184 | BOOL bRc; | ^~~ sqlite/sqlite3.c: In function 'sqlite3DefaultRowEst': sqlite/sqlite3.c:109169:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 109169 | if( pIdx->pPartIdxWhere!=0 ) a[0] -= 10; assert( 10==sqlite3LogEst(2) ); | ^~ In file included from sqlite/sqlite3.c:13475: sqlite/sqlite3.c:109169:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 109169 | if( pIdx->pPartIdxWhere!=0 ) a[0] -= 10; assert( 10==sqlite3LogEst(2) ); | ^~~~~~ sqlite/sqlite3.c:109170:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 109170 | if( a[0]<33 ) a[0] = 33; assert( 33==sqlite3LogEst(10) ); | ^~ sqlite/sqlite3.c:109170:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 109170 | if( a[0]<33 ) a[0] = 33; assert( 33==sqlite3LogEst(10) ); | ^~~~~~ sqlite/sqlite3.c: In function 'whereRangeScanEst': sqlite/sqlite3.c:139936:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 139936 | if( iLwrIdx==iUprIdx ) nNew -= 20; assert( 20==sqlite3LogEst(4) ); | ^~ sqlite/sqlite3.c:139936:47: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 139936 | if( iLwrIdx==iUprIdx ) nNew -= 20; assert( 20==sqlite3LogEst(4) ); | ^~~~~~ sqlite/sqlite3.c: In function 'sqlite3SelectNew': sqlite/sqlite3.c:123307:10: warning: function may return address of local variable [-Wreturn-local-addr] 123307 | return pNew; | ^~~~ sqlite/sqlite3.c:123267:10: note: declared here 123267 | Select standin; | ^~~~~~~ sqlite/sqlite3.c: In function 'sqlite3Fts5IndexQuery': sqlite/sqlite3.c:210681:18: warning: 'memcpy' specified bound 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 210681 | if( nToken ) memcpy(&buf.p[1], pToken, nToken); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -shared -s -static-libgcc -o seqminer.dll tmp.def BCFReader.o BGenFile.o BGenIndex.o BGenVariant.o Exception.o FileIO.o GeneLoader.o MmapFile.o PatternMatch.o PeopleSet.o PlinkInputFile.o PlinkOutputFile.o Profiler.o R_CPP_interface.o RangeList.o Rannotation.o SimpleMatrix.o SingleChromosomeBCFIndex.o SingleChromosomeVCFIndex.o TypeConversion.o Utils.o VCFHeader.o VCFIndividual.o VCFInfo.o VCFInputFile.o VCFUtil.o bcf.o bcf_index.o bcfutils.o bedidx.o bgen2genoLoader.o bgzf.o knetfile.o kstring.o plink2genoLoader.o rvMetaLoader.o scbcf2genoLoader.o scvcf2genoLoader.o seqForStat.o seqminer.o seqminer_init.o tabixLoader.o tabix_index.o vcf.o vcf2genoLoader.o -lz -lws2_32 zstd/lib/common/debug.o zstd/lib/common/entropy_common.o zstd/lib/common/error_private.o zstd/lib/common/fse_decompress.o zstd/lib/common/pool.o zstd/lib/common/threading.o zstd/lib/common/xxhash.o zstd/lib/common/zstd_common.o zstd/lib/compress/fse_compress.o zstd/lib/compress/hist.o zstd/lib/compress/huf_compress.o zstd/lib/compress/zstd_compress.o zstd/lib/compress/zstd_double_fast.o zstd/lib/compress/zstd_fast.o zstd/lib/compress/zstd_lazy.o zstd/lib/compress/zstd_ldm.o zstd/lib/compress/zstd_opt.o zstd/lib/compress/zstdmt_compress.o zstd/lib/decompress/huf_decompress.o zstd/lib/decompress/zstd_decompress.o zstd/lib/deprecated/zbuff_common.o zstd/lib/deprecated/zbuff_compress.o zstd/lib/deprecated/zbuff_decompress.o zstd/lib/dictBuilder/cover.o zstd/lib/dictBuilder/divsufsort.o zstd/lib/dictBuilder/fastcover.o zstd/lib/dictBuilder/zdict.o zstd/lib/legacy/zstd_v05.o zstd/lib/legacy/zstd_v06.o zstd/lib/legacy/zstd_v07.o sqlite/sqlite3.o -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-seqminer/00new/seqminer/libs/x64 ** R ** demo ** 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 (seqminer)