* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘seqminer’ ...
** package ‘seqminer’ successfully unpacked and MD5 sums checked
** 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 14.2.0-8) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpJW1M7C/R.INSTALL1c163f6b9d5505/seqminer/src'
have SQLite
have bzip2
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BCFReader.cpp -o BCFReader.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BGenFile.cpp -o BGenFile.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BGenIndex.cpp -o BGenIndex.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BGenVariant.cpp -o BGenVariant.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Exception.cpp -o Exception.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c FileIO.cpp -o FileIO.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c GeneLoader.cpp -o GeneLoader.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MmapFile.cpp -o MmapFile.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PatternMatch.cpp -o PatternMatch.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PeopleSet.cpp -o PeopleSet.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PlinkInputFile.cpp -o PlinkInputFile.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PlinkOutputFile.cpp -o PlinkOutputFile.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Profiler.cpp -o Profiler.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c R_CPP_interface.cpp -o R_CPP_interface.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RangeList.cpp -o RangeList.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Rannotation.cpp -o Rannotation.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SimpleMatrix.cpp -o SimpleMatrix.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SingleChromosomeBCFIndex.cpp -o SingleChromosomeBCFIndex.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SingleChromosomeVCFIndex.cpp -o SingleChromosomeVCFIndex.o
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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c TypeConversion.cpp -o TypeConversion.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Utils.cpp -o Utils.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFHeader.cpp -o VCFHeader.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFIndividual.cpp -o VCFIndividual.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFInfo.cpp -o VCFInfo.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFInputFile.cpp -o VCFInputFile.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFUtil.cpp -o VCFUtil.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bgen2genoLoader.cpp -o bgen2genoLoader.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rvMetaLoader.cpp -o rvMetaLoader.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scvcf2genoLoader.cpp -o scvcf2genoLoader.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tabixLoader.cpp -o tabixLoader.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -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.check/r-patched-gcc/Work/build/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 -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c vcf2genoLoader.cpp -o vcf2genoLoader.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpJW1M7C/R.INSTALL1c163f6b9d5505/seqminer/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpJW1M7C/R.INSTALL1c163f6b9d5505/seqminer/src'
have SQLite
have bzip2
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpJW1M7C/R.INSTALL1c163f6b9d5505/seqminer/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-seqminer/00new/seqminer/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘seqminer’
finding HTML links ... done
SEQMINER html
addJob html
annotateGene html
annotatePlain html
annotateVcf html
createSingleChromosomeBCFIndex html
createSingleChromosomeVCFIndex html
download.annotation.resource html
getCovPair html
getRefBase html
hasIndex html
isDirWritable html
isInRange html
isTabixRange html
isURL html
makeAnnotationParameter html
newJob html
newWorkflow html
openPlink html
readBGENToListByGene html
readBGENToListByRange html
readBGENToMatrixByGene html
readBGENToMatrixByRange html
readPlinkToMatrixByIndex html
readSingleChromosomeBCFToMatrixByRange
html
readSingleChromosomeVCFToMatrixByRange
html
readVCFToListByGene html
readVCFToListByRange html
readVCFToMatrixByGene html
readVCFToMatrixByRange html
rvmeta.readCovByRange html
rvmeta.readDataByGene html
rvmeta.readDataByRange html
rvmeta.readNullModel html
rvmeta.readScoreByRange html
rvmeta.readSkewByRange html
rvmeta.writeCovData html
rvmeta.writeScoreData html
sub-.PlinkFile html
tabix.createIndex html
tabix.createIndex.meta html
tabix.createIndex.vcf html
tabix.read html
tabix.read.header html
tabix.read.table html
validateAnnotationParameter html
verifyFilename html
writeWorkflow html
** 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)