* installing *source* package ‘seqminer’ ...
** using staged installation
configure: CC = gcc-14
configure: CFLAGS = -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native
configure: CXX = g++-14 -std=gnu++11
configure: CXXFLAGS = -g -O2 -Wall -pedantic -mtune=native
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 g++-14 -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... g++-14 -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: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
using C++17
have SQLite
have bzip2
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c BCFReader.cpp -o BCFReader.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c BGenFile.cpp -o BGenFile.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c BGenIndex.cpp -o BGenIndex.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c BGenVariant.cpp -o BGenVariant.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c Exception.cpp -o Exception.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c FileIO.cpp -o FileIO.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c GeneLoader.cpp -o GeneLoader.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c MmapFile.cpp -o MmapFile.o
MmapFile.cpp:3:9: warning: "STRICT_R_HEADERS" redefined
    3 | #define STRICT_R_HEADERS
      |         ^~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c PatternMatch.cpp -o PatternMatch.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c PeopleSet.cpp -o PeopleSet.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c PlinkInputFile.cpp -o PlinkInputFile.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c PlinkOutputFile.cpp -o PlinkOutputFile.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c Profiler.cpp -o Profiler.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c R_CPP_interface.cpp -o R_CPP_interface.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c RangeList.cpp -o RangeList.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c Rannotation.cpp -o Rannotation.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c SimpleMatrix.cpp -o SimpleMatrix.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c SingleChromosomeBCFIndex.cpp -o SingleChromosomeBCFIndex.o
SingleChromosomeBCFIndex.cpp:3:9: warning: "STRICT_R_HEADERS" redefined
    3 | #define STRICT_R_HEADERS
      |         ^~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c SingleChromosomeVCFIndex.cpp -o SingleChromosomeVCFIndex.o
SingleChromosomeVCFIndex.cpp:3:9: warning: "STRICT_R_HEADERS" redefined
    3 | #define STRICT_R_HEADERS
      |         ^~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
SingleChromosomeVCFIndex.cpp: In member function ‘int SingleChromosomeVCFIndex::createIndex()’:
SingleChromosomeVCFIndex.cpp:69:15: warning: unused variable ‘fn’ [-Wunused-variable]
   69 |   const char* fn = vcfFile_.c_str();
      |               ^~
SingleChromosomeVCFIndex.cpp: In member function ‘int SingleChromosomeVCFIndex::mapIndex()’:
SingleChromosomeVCFIndex.cpp:201:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare]
  201 |   if (Nrecord != d[1]) {
      |       ~~~~~~~~^~~~~~~
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c TypeConversion.cpp -o TypeConversion.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c Utils.cpp -o Utils.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c VCFHeader.cpp -o VCFHeader.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c VCFIndividual.cpp -o VCFIndividual.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c VCFInfo.cpp -o VCFInfo.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c VCFInputFile.cpp -o VCFInputFile.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c VCFUtil.cpp -o VCFUtil.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c bcf.c -o bcf.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c bcf_index.c -o bcf_index.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c bcfutils.c -o bcfutils.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c bedidx.c -o bedidx.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c bgen2genoLoader.cpp -o bgen2genoLoader.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c bgzf.c -o bgzf.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c knetfile.c -o knetfile.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c kstring.c -o kstring.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c plink2genoLoader.cpp -o plink2genoLoader.o
plink2genoLoader.cpp: In function ‘int readBedToMatrixByIndex(const std::string&, int, int, const std::vector<int>&, const std::vector<int>&, SEXP)’:
plink2genoLoader.cpp:126:3: warning: ‘snpMajorMode’ may be used uninitialized [-Wmaybe-uninitialized]
  126 |   if (snpMajorMode) {
      |   ^~
plink2genoLoader.cpp:78:8: note: ‘snpMajorMode’ was declared here
   78 |   bool snpMajorMode;
      |        ^~~~~~~~~~~~
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c rvMetaLoader.cpp -o rvMetaLoader.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scbcf2genoLoader.cpp -o scbcf2genoLoader.o
scbcf2genoLoader.cpp: In function ‘int parseBCFVariant(const BCFHeader&, uint32_t, uint32_t, std::vector<char>, std::vector<double>*, std::vector<std::__cxx11::basic_string<char> >*)’:
scbcf2genoLoader.cpp:287:10: warning: unused variable ‘format_type’ [-Wunused-variable]
  287 |   int8_t format_type = *pIndv;
      |          ^~~~~~~~~~~
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scvcf2genoLoader.cpp -o scvcf2genoLoader.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seqForStat.c -o seqForStat.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seqminer.c -o seqminer.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seqminer_init.c -o seqminer_init.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c tabixLoader.cpp -o tabixLoader.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c tabix_index.c -o tabix_index.o
tabix_index.c:19:14: warning: ‘currentTime’ defined but not used [-Wunused-function]
   19 | static char* currentTime(void) {
      |              ^~~~~~~~~~~
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c vcf.c -o vcf.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c vcf2genoLoader.cpp -o vcf2genoLoader.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/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-gcc-14/lib -lR
have SQLite
have bzip2
installing to /home/hornik/tmp/CRAN_recheck/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)