* installing *source* package ‘seqminer’ ... ** using staged installation configure: CC = clang-18 configure: CFLAGS = -g -O3 -Wall -pedantic configure: CXX = clang++-18 -std=gnu++11 configure: CXXFLAGS = -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion 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++-18 -std=gnu++11 accepts -g... yes checking how to run the C++ preprocessor... clang++-18 -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... 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: ‘Debian clang version 18.1.8 (11)’ using C++ compiler: ‘Debian clang version 18.1.8 (11)’ using C++17 have bzip2 clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c BCFReader.cpp -o BCFReader.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) \ | ^~~~~~~~~~~ 3 warnings generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c BGenFile.cpp -o BGenFile.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c BGenIndex.cpp -o BGenIndex.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c BGenVariant.cpp -o BGenVariant.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c Exception.cpp -o Exception.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c FileIO.cpp -o FileIO.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c GeneLoader.cpp -o GeneLoader.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c MmapFile.cpp -o MmapFile.o MmapFile.cpp:3:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 3 | #define STRICT_R_HEADERS | ^ :16:9: note: previous definition is here 16 | #define STRICT_R_HEADERS 1 | ^ 1 warning generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c PatternMatch.cpp -o PatternMatch.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c PeopleSet.cpp -o PeopleSet.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c PlinkInputFile.cpp -o PlinkInputFile.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c PlinkOutputFile.cpp -o PlinkOutputFile.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 | ^ 1 warning generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c Profiler.cpp -o Profiler.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c R_CPP_interface.cpp -o R_CPP_interface.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c RangeList.cpp -o RangeList.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c Rannotation.cpp -o Rannotation.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c SimpleMatrix.cpp -o SimpleMatrix.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c SingleChromosomeBCFIndex.cpp -o SingleChromosomeBCFIndex.o SingleChromosomeBCFIndex.cpp:3:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 3 | #define STRICT_R_HEADERS | ^ :16:9: note: previous definition is here 16 | #define STRICT_R_HEADERS 1 | ^ 1 warning generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c SingleChromosomeVCFIndex.cpp -o SingleChromosomeVCFIndex.o SingleChromosomeVCFIndex.cpp:3:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 3 | #define STRICT_R_HEADERS | ^ :16:9: note: previous definition is here 16 | #define STRICT_R_HEADERS 1 | ^ SingleChromosomeVCFIndex.cpp:69:15: warning: unused variable 'fn' [-Wunused-variable] 69 | const char* fn = vcfFile_.c_str(); | ^~ 2 warnings generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c TypeConversion.cpp -o TypeConversion.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c Utils.cpp -o Utils.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c VCFHeader.cpp -o VCFHeader.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c VCFIndividual.cpp -o VCFIndividual.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c VCFInfo.cpp -o VCFInfo.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c VCFInputFile.cpp -o VCFInputFile.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c VCFUtil.cpp -o VCFUtil.o 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 | ^ 1 warning generated. clang-18 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c bcf.c -o bcf.o clang-18 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c bcf_index.c -o bcf_index.o clang-18 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c bcfutils.c -o bcfutils.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) \ | ^~~~~~~~~~~~~~~ :20:1: note: expanded from here 20 | 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) \ | ^~~~~~~~~~~~~ :34:1: note: expanded from here 34 | kh_del_str2id | ^~~~~~~~~~~~~ 2 warnings generated. clang-18 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c bedidx.c -o bedidx.o 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) \ | ^~~~~~~~~~~~~~~ :8:1: note: expanded from here 8 | 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) \ | ^~~~~~~~~~~~~ :22:1: note: expanded from here 22 | kh_del_reg | ^~~~~~~~~~ 2 warnings generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c bgen2genoLoader.cpp -o bgen2genoLoader.o clang-18 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c bgzf.c -o bgzf.o clang-18 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c knetfile.c -o knetfile.o clang-18 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c kstring.c -o kstring.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c plink2genoLoader.cpp -o plink2genoLoader.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c rvMetaLoader.cpp -o rvMetaLoader.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 | ^ rvMetaLoader.cpp:1868:7: warning: variable 'lineRead' set but not used [-Wunused-but-set-variable] 1868 | int lineRead = 0; | ^ 2 warnings generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c scbcf2genoLoader.cpp -o scbcf2genoLoader.o scbcf2genoLoader.cpp:287:10: warning: unused variable 'format_type' [-Wunused-variable] 287 | int8_t format_type = *pIndv; | ^~~~~~~~~~~ 1 warning generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c scvcf2genoLoader.cpp -o scvcf2genoLoader.o clang-18 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c seqForStat.c -o seqForStat.o clang-18 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c seqminer.c -o seqminer.o clang-18 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c seqminer_init.c -o seqminer_init.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c tabixLoader.cpp -o tabixLoader.o clang-18 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c tabix_index.c -o tabix_index.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) \ | ^~~~~~~~~~~~~~~ :43:1: note: expanded from here 43 | kh_clear_i | ^~~~~~~~~~ tabix_index.c:48:1: warning: unused function 'kh_del_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:259:21: note: expanded from macro 'KHASH_INIT' 259 | static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ | ^~~~~~~~~~~~~ :57:1: note: expanded from here 57 | 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) \ | ^~~~~~~~~~~~~~~ :72:1: note: expanded from here 72 | 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) \ | ^~~~~~~~~~~~~ :86:1: note: expanded from here 86 | kh_del_s | ^~~~~~~~ 6 warnings generated. clang-18 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c vcf.c -o vcf.o vcf.c:12:1: warning: unused function 'ks_getc' [-Wunused-function] 12 | 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) \ | ^~~~~~~ 1 warning generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c vcf2genoLoader.cpp -o vcf2genoLoader.o 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. clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-18/lib -Wl,-O1 -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 -L/home/hornik/tmp/R-d-clang-18/lib -lR have bzip2 installing to /srv/hornik/tmp/CRAN_pretest/seqminer.Rcheck/00LOCK-seqminer/00new/seqminer/libs ** 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)