* installing *source* package ‘seqminer’ ...
** this is package ‘seqminer’ version ‘9.9’
** package ‘seqminer’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC = clang -arch arm64 -std=gnu23
configure: CFLAGS = -falign-functions=64 -Wall -g -O2
configure: CXX = clang++ -arch arm64 -std=gnu++17
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 arm64 -std=gnu++17 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -arch arm64 -std=gnu++17 -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
specified C++17
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
using C++17
using SDK: ‘MacOSX14.5.sdk’
have SQLite
have bzip2
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BCFReader.cpp -o BCFReader.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BGenFile.cpp -o BGenFile.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BGenIndex.cpp -o BGenIndex.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BGenVariant.cpp -o BGenVariant.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Exception.cpp -o Exception.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FileIO.cpp -o FileIO.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GeneLoader.cpp -o GeneLoader.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MmapFile.cpp -o MmapFile.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/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]
18 | KSTREAM_INIT(gzFile, gzread, 4096)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./kseq.h:145:2: note: expanded from macro 'KSTREAM_INIT'
145 | __KS_BASIC(type_t, __bufsize) \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./kseq.h:58:21: note: expanded from macro '__KS_BASIC'
58 | static inline void ks_destroy(kstream_t *ks) \
| ^~~~~~~~~~
BCFReader.cpp:18:1: warning: unused function 'ks_getc' [-Wunused-function]
18 | KSTREAM_INIT(gzFile, gzread, 4096)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
146 | __KS_GETC(__read, __bufsize) \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
./kseq.h:67:20: note: expanded from macro '__KS_GETC'
67 | static inline int ks_getc(kstream_t *ks) \
| ^~~~~~~
BCFReader.cpp:18:1: warning: unused function 'ks_getuntil' [-Wunused-function]
18 | KSTREAM_INIT(gzFile, gzread, 4096)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
147 | __KS_GETUNTIL(__read, __bufsize)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./kseq.h:140:20: note: expanded from macro '__KS_GETUNTIL'
140 | static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
| ^~~~~~~~~~~
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PeopleSet.cpp -o PeopleSet.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PlinkInputFile.cpp -o PlinkInputFile.o
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PlinkOutputFile.cpp -o PlinkOutputFile.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Profiler.cpp -o Profiler.o
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]
65 | double nMiss = 0; // number of missing
| ^
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_CPP_interface.cpp -o R_CPP_interface.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]
77 | #pragma message "Use native Apple Timer"
| ^
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RangeList.cpp -o RangeList.o
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rannotation.cpp -o Rannotation.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SimpleMatrix.cpp -o SimpleMatrix.o
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SingleChromosomeBCFIndex.cpp -o SingleChromosomeBCFIndex.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SingleChromosomeVCFIndex.cpp -o SingleChromosomeVCFIndex.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c TypeConversion.cpp -o TypeConversion.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Utils.cpp -o Utils.o
SingleChromosomeVCFIndex.cpp:69:15: warning: unused variable 'fn' [-Wunused-variable]
69 | const char* fn = vcfFile_.c_str();
| ^~
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c VCFHeader.cpp -o VCFHeader.o
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c VCFIndividual.cpp -o VCFIndividual.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c VCFInfo.cpp -o VCFInfo.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c VCFInputFile.cpp -o VCFInputFile.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c VCFUtil.cpp -o VCFUtil.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/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 arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/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 arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c bcfutils.c -o bcfutils.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c bedidx.c -o bedidx.o
bcfutils.c:11:1: warning: unused function 'kh_clear_str2id' [-Wunused-function]
11 | KHASH_MAP_INIT_STR(str2id, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
484 | 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'
140 | static inline void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:66:1: note: expanded from here
66 | kh_clear_str2id
| ^~~~~~~~~~~~~~~
bcfutils.c:11:1: warning: unused function 'kh_del_str2id' [-Wunused-function]
11 | KHASH_MAP_INIT_STR(str2id, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
484 | 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'
259 | static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:80:1: note: expanded from here
80 | kh_del_str2id
| ^~~~~~~~~~~~~
bedidx.c:23:1: warning: unused function 'kh_clear_reg' [-Wunused-function]
23 | KHASH_MAP_INIT_STR(reg, bed_reglist_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
484 | 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'
140 | static inline void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:467:1: note: expanded from here
467 | kh_clear_reg
| ^~~~~~~~~~~~
bedidx.c:23:1: warning: unused function 'kh_del_reg' [-Wunused-function]
23 | KHASH_MAP_INIT_STR(reg, bed_reglist_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
484 | 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'
259 | static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:481:1: note: expanded from here
481 | 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]
65 | double nMiss = 0; // number of missing
| ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bgen2genoLoader.cpp -o bgen2genoLoader.o
2 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/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 arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/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 arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c plink2genoLoader.cpp -o plink2genoLoader.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rvMetaLoader.cpp -o rvMetaLoader.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/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]
65 | double nMiss = 0; // number of missing
| ^
scbcf2genoLoader.cpp:287:10: warning: unused variable 'format_type' [-Wunused-variable]
287 | int8_t format_type = *pIndv;
| ^~~~~~~~~~~
rvMetaLoader.cpp:1868:7: warning: variable 'lineRead' set but not used [-Wunused-but-set-variable]
1868 | int lineRead = 0;
| ^
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scvcf2genoLoader.cpp -o scvcf2genoLoader.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/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 arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/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 arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tabixLoader.cpp -o tabixLoader.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/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
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/include -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c vcf.c -o vcf.o
tabix_index.c:146:25: warning: variable 'ncols' set but not used [-Wunused-but-set-variable]
146 | int i, b = 0, id = 1, ncols = 0;
| ^
tabix_index.c:19:14: warning: unused function 'currentTime' [-Wunused-function]
19 | static char* currentTime(void) {
| ^~~~~~~~~~~
tabix_index.c:48:1: warning: unused function 'kh_clear_i' [-Wunused-function]
48 | KHASH_MAP_INIT_INT(i, ti_binlist_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
453 | 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'
140 | static inline void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:44:1: note: expanded from here
44 | kh_clear_i
| ^~~~~~~~~~
tabix_index.c:48:1: warning: unused function 'kh_del_i' [-Wunused-function]
48 | KHASH_MAP_INIT_vcf.c:12:1:INT(i warning: unused function 'ks_getc' [-Wunused-function]
, ti_binlis 12 | KSTREAM_INIT(gzFilt_t)
e, gzread, 40| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT'./kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
453 | KH
ASH 146 | _I __KS_GETC(NIT(__reaname, uint32_t, khd, __buval_tfsize) \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
, 1, kh_in./kseq.h:67:20: note: expanded from macro '__KS_GETC'
t_ha 67 | static sh_func, kh_int_inline int ks_getc(kstrehash_eqam_t *ks)ual)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
\
| ^~~~~~~
./khash.h:259:21: note: expanded from macro 'KHASH_INIT'
259 | static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:58:1: note: expanded from here
58 | kh_del_i
| ^~~~~~~~
tabix_index.c:49:1: warning: unused function 'kh_clear_s' [-Wunused-function]
49 | KHASH_MAP_INIT_STR(s, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
484 | 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'
140 | static inline void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:73:1: note: expanded from here
73 | kh_clear_s
| ^~~~~~~~~~
tabix_index.c:49:1: warning: unused function 'kh_del_s' [-Wunused-function]
49 | KHASH_MAP_INIT_STR(s, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
484 | 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'
259 | static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:87:1: note: expanded from here
87 | kh_del_s
| ^~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -I. -falign-functions=64 -Wall -g -O2 -DHAVE_SQLITE -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 -DR_NO_REMAP -I/opt/R/arm64/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]
65 | double nMiss = 0; // number of missing
| ^
vcf2genoLoader.cpp:294:7: warning: variable 'nonVariantSite' set but not used [-Wunused-but-set-variable]
294 | int nonVariantSite = 0;
| ^
2 warnings generated.
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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
ld: warning: ignoring duplicate libraries: '-lsqlite3', '-lzstd'
have SQLite
have bzip2
installing to /Volumes/Builds/packages/sonoma-arm64/results/4.6/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)