* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘seqminer’ ...
** package ‘seqminer’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC = clang-19
configure: CFLAGS = -g -O3 -Wall -pedantic
configure: CXX = clang++-19 -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++-19 -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... clang++-19 -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 19.1.5 (1)’
using C++ compiler: ‘Debian clang version 19.1.5 (1)’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpPSc8xa/R.INSTALL2a74d9686ca3f6/seqminer/src'
have SQLite
have bzip2
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -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++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c BGenFile.cpp -o BGenFile.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c BGenIndex.cpp -o BGenIndex.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c BGenVariant.cpp -o BGenVariant.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c Exception.cpp -o Exception.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c FileIO.cpp -o FileIO.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c GeneLoader.cpp -o GeneLoader.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c MmapFile.cpp -o MmapFile.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c PatternMatch.cpp -o PatternMatch.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c PeopleSet.cpp -o PeopleSet.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c PlinkInputFile.cpp -o PlinkInputFile.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -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++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c Profiler.cpp -o Profiler.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c R_CPP_interface.cpp -o R_CPP_interface.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c RangeList.cpp -o RangeList.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c Rannotation.cpp -o Rannotation.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c SimpleMatrix.cpp -o SimpleMatrix.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c SingleChromosomeBCFIndex.cpp -o SingleChromosomeBCFIndex.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c SingleChromosomeVCFIndex.cpp -o SingleChromosomeVCFIndex.o
SingleChromosomeVCFIndex.cpp:69:15: warning: unused variable 'fn' [-Wunused-variable]
69 | const char* fn = vcfFile_.c_str();
| ^~
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c TypeConversion.cpp -o TypeConversion.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c Utils.cpp -o Utils.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c VCFHeader.cpp -o VCFHeader.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c VCFIndividual.cpp -o VCFIndividual.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c VCFInfo.cpp -o VCFInfo.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c VCFInputFile.cpp -o VCFInputFile.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -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-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c bcf.c -o bcf.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c bcf_index.c -o bcf_index.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -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) \
| ^~~~~~~~~~~~~~~
<scratch space>:30:1: note: expanded from here
30 | kh_clear_str2id
| ^~~~~~~~~~~~~~~
bcfutils.c:11:1: warning: unused function 'kh_del_str2id' [-Wunused-function]
11 | KHASH_MAP_INIT_STR(str2id, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
484 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:259:21: note: expanded from macro 'KHASH_INIT'
259 | static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:44:1: note: expanded from here
44 | kh_del_str2id
| ^~~~~~~~~~~~~
2 warnings generated.
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -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) \
| ^~~~~~~~~~~~~~~
<scratch space>:14:1: note: expanded from here
14 | kh_clear_reg
| ^~~~~~~~~~~~
bedidx.c:23:1: warning: unused function 'kh_del_reg' [-Wunused-function]
23 | KHASH_MAP_INIT_STR(reg, bed_reglist_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
484 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:259:21: note: expanded from macro 'KHASH_INIT'
259 | static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:28:1: note: expanded from here
28 | kh_del_reg
| ^~~~~~~~~~
2 warnings generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c bgen2genoLoader.cpp -o bgen2genoLoader.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c bgzf.c -o bgzf.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c knetfile.c -o knetfile.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c kstring.c -o kstring.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c plink2genoLoader.cpp -o plink2genoLoader.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -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++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -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++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c scvcf2genoLoader.cpp -o scvcf2genoLoader.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c seqForStat.c -o seqForStat.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c seqminer.c -o seqminer.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -fpic -g -O3 -Wall -pedantic -c seqminer_init.c -o seqminer_init.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -O3 -Wall -pedantic -DR_NO_REMAP -c tabixLoader.cpp -o tabixLoader.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -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) \
| ^~~~~~~~~~~~~~~
<scratch space>:53:1: note: expanded from here
53 | 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) \
| ^~~~~~~~~~~~~
<scratch space>:67:1: note: expanded from here
67 | kh_del_i
| ^~~~~~~~
tabix_index.c:49:1: warning: unused function 'kh_clear_s' [-Wunused-function]
49 | KHASH_MAP_INIT_STR(s, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
484 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:140:21: note: expanded from macro 'KHASH_INIT'
140 | static inline void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:82:1: note: expanded from here
82 | kh_clear_s
| ^~~~~~~~~~
tabix_index.c:49:1: warning: unused function 'kh_del_s' [-Wunused-function]
49 | KHASH_MAP_INIT_STR(s, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
484 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:259:21: note: expanded from macro 'KHASH_INIT'
259 | static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:96:1: note: expanded from here
96 | kh_del_s
| ^~~~~~~~
6 warnings generated.
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -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++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 -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++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/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-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpPSc8xa/R.INSTALL2a74d9686ca3f6/seqminer/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpPSc8xa/R.INSTALL2a74d9686ca3f6/seqminer/src'
have SQLite
have bzip2
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpPSc8xa/R.INSTALL2a74d9686ca3f6/seqminer/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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)