* installing *source* package ‘seqminer’ ... ** package ‘seqminer’ successfully unpacked and MD5 sums checked ** using staged installation configure: CC = clang -arch x86_64 configure: CFLAGS = -falign-functions=64 -Wall -g -O2 configure: CXX = clang++ -arch x86_64 -std=gnu++11 configure: CXXFLAGS = -falign-functions=64 -Wall -g -O2 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 we are using the GNU C++ compiler... yes checking whether clang++ -arch x86_64 -std=gnu++11 accepts -g... yes checking how to run the C++ preprocessor... clang++ -arch x86_64 -std=gnu++11 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... rm: conftest.dSYM: is a directory rm: conftest.dSYM: is a directory yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for BZ2_bzDecompressInit in -lbz2... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes configure: Will use system-wide bzip2 library checking for ZSTD_compress in -lzstd... yes checking zstd.h usability... yes checking zstd.h presence... yes checking for zstd.h... yes configure: Will use system-wide zstd library checking for sqlite3_open in -lsqlite3... yes checking sqlite3.h usability... yes checking sqlite3.h presence... yes checking for sqlite3.h... yes configure: Will use system-wide sqlite library checking for regcomp in -lc... yes checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking for working REG_STARTEND... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/config.h ** libs using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ have bzip2 clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BCFReader.cpp -o BCFReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BGenFile.cpp -o BGenFile.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BGenIndex.cpp -o BGenIndex.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BGenVariant.cpp -o BGenVariant.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Exception.cpp -o Exception.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FileIO.cpp -o FileIO.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GeneLoader.cpp -o GeneLoader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MmapFile.cpp -o MmapFile.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PatternMatch.cpp -o PatternMatch.o BCFReader.cpp:18:1: warning: unused function 'ks_destroy' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 4096) ^ ./kseq.h:145:2: note: expanded from macro 'KSTREAM_INIT' __KS_BASIC(type_t, __bufsize) \ ^ ./kseq.h:58:21: note: expanded from macro '__KS_BASIC' static inline void ks_destroy(kstream_t *ks) \ ^ BCFReader.cpp:18:1: warning: unused function 'ks_getc' [-Wunused-function] ./kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ ./kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ BCFReader.cpp:18:1: warning: unused function 'ks_getuntil' [-Wunused-function] ./kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETUNTIL(__read, __bufsize) ^ ./kseq.h:140:20: note: expanded from macro '__KS_GETUNTIL' static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \ ^ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PeopleSet.cpp -o PeopleSet.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PlinkInputFile.cpp -o PlinkInputFile.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PlinkOutputFile.cpp -o PlinkOutputFile.o 3 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Profiler.cpp -o Profiler.o In file included from Profiler.cpp:1: In file included from ./Profiler.h:7: ./SimpleTimer.h:77:9: warning: Use native Apple Timer [-W#pragma-messages] #pragma message "Use native Apple Timer" ^ In file included from PlinkOutputFile.cpp:1: In file included from ./PlinkOutputFile.h:4: In file included from ./VCFUtil.h:12: ./VCFExtractor.h:65:14: warning: variable 'nMiss' set but not used [-Wunused-but-set-variable] double nMiss = 0; // number of missing ^ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_CPP_interface.cpp -o R_CPP_interface.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RangeList.cpp -o RangeList.o 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rannotation.cpp -o Rannotation.o 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SimpleMatrix.cpp -o SimpleMatrix.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SingleChromosomeBCFIndex.cpp -o SingleChromosomeBCFIndex.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SingleChromosomeVCFIndex.cpp -o SingleChromosomeVCFIndex.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c TypeConversion.cpp -o TypeConversion.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Utils.cpp -o Utils.o SingleChromosomeVCFIndex.cpp:69:15: warning: unused variable 'fn' [-Wunused-variable] const char* fn = vcfFile_.c_str(); ^ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c VCFHeader.cpp -o VCFHeader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c VCFIndividual.cpp -o VCFIndividual.o 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c VCFInfo.cpp -o VCFInfo.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c VCFInputFile.cpp -o VCFInputFile.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c VCFUtil.cpp -o VCFUtil.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c bcf.c -o bcf.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c bcf_index.c -o bcf_index.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c bcfutils.c -o bcfutils.o bcfutils.c:11:1: warning: unused function 'kh_clear_str2id' [-Wunused-function] KHASH_MAP_INIT_STR(str2id, int) ^ ./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:140:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :15:1: note: expanded from here kh_clear_str2id ^ bcfutils.c:11:1: warning: unused function 'kh_del_str2id' [-Wunused-function] ./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:259:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :29:1: note: expanded from here kh_del_str2id ^ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c bedidx.c -o bedidx.o bedidx.c:23:1: warning: unused function 'kh_clear_reg' [-Wunused-function] KHASH_MAP_INIT_STR(reg, bed_reglist_t) ^ ./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:140:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :426:1: note: expanded from here kh_clear_reg ^ bedidx.c:23:1: warning: unused function 'kh_del_reg' [-Wunused-function] ./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:259:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :440:1: note: expanded from here kh_del_reg ^ In file included from VCFUtil.cpp:1: In file included from ./VCFUtil.h:12: ./VCFExtractor.h:65:14: warning: variable 'nMiss' set but not used [-Wunused-but-set-variable] double nMiss = 0; // number of missing ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bgen2genoLoader.cpp -o bgen2genoLoader.o 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c bgzf.c -o bgzf.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c knetfile.c -o knetfile.o 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c kstring.c -o kstring.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c plink2genoLoader.cpp -o plink2genoLoader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rvMetaLoader.cpp -o rvMetaLoader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scbcf2genoLoader.cpp -o scbcf2genoLoader.o In file included from rvMetaLoader.cpp:9: In file included from ./VCFUtil.h:12: ./VCFExtractor.h:65:14: warning: variable 'nMiss' set but not used [-Wunused-but-set-variable] double nMiss = 0; // number of missing ^ scbcf2genoLoader.cpp:287:10: warning: unused variable 'format_type' [-Wunused-variable] int8_t format_type = *pIndv; ^ rvMetaLoader.cpp:1868:7: warning: variable 'lineRead' set but not used [-Wunused-but-set-variable] int lineRead = 0; ^ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scvcf2genoLoader.cpp -o scvcf2genoLoader.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c seqForStat.c -o seqForStat.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c seqminer.c -o seqminer.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c seqminer_init.c -o seqminer_init.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tabixLoader.cpp -o tabixLoader.o 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c tabix_index.c -o tabix_index.o tabix_index.c:146:25: warning: variable 'ncols' set but not used [-Wunused-but-set-variable] int i, b = 0, id = 1, ncols = 0; ^ tabix_index.c:19:14: warning: unused function 'currentTime' [-Wunused-function] static char* currentTime(void) { ^ tabix_index.c:48:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, ti_binlist_t) ^ ./khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ ./khash.h:140:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :48:1: note: expanded from here kh_clear_i ^ tabix_index.c:48:1: warning: unused function 'kh_del_i' [-Wunused-function] ./khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ ./khash.h:259:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :62:1: note: expanded from here kh_del_i ^ tabix_index.c:49:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ ./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:140:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :77:1: note: expanded from here kh_clear_s ^ tabix_index.c:49:1: warning: unused function 'kh_del_s' [-Wunused-function] ./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:259:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :91:1: note: expanded from here kh_del_s ^ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c vcf.c -o vcf.o vcf.c:12:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 4096) ^ ./kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ ./kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vcf2genoLoader.cpp -o vcf2genoLoader.o 6 warnings generated. In file included from vcf2genoLoader.cpp:10: In file included from ./VCFUtil.h:12: ./VCFExtractor.h:65:14: warning: variable 'nMiss' set but not used [-Wunused-but-set-variable] double nMiss = 0; // number of missing ^ vcf2genoLoader.cpp:294:7: warning: variable 'nonVariantSite' set but not used [-Wunused-but-set-variable] int nonVariantSite = 0; ^ 2 warnings generated. 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o seqminer.so 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 -lm -lbz2 -lzstd -lsqlite3 -lzstd -lsqlite3 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation have bzip2 /Volumes/Builds/packages/big-sur-x86_64/results/4.3/seqminer.Rcheck/00_pkg_src/seqminer/src/Exception.o: no symbols /Volumes/Builds/packages/big-sur-x86_64/results/4.3/seqminer.Rcheck/00_pkg_src/seqminer/src/PatternMatch.o: no symbols /Volumes/Builds/packages/big-sur-x86_64/results/4.3/seqminer.Rcheck/00_pkg_src/seqminer/src/Utils.o: no symbols /Volumes/Builds/packages/big-sur-x86_64/results/4.3/seqminer.Rcheck/00_pkg_src/seqminer/src/VCFHeader.o: no symbols /Volumes/Builds/packages/big-sur-x86_64/results/4.3/seqminer.Rcheck/00_pkg_src/seqminer/src/VCFUtil.o: no symbols installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.3/seqminer.Rcheck/00LOCK-seqminer/00new/seqminer/libs ** generating debug symbols (dSYM) ** 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 ** 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 (seqminer)