* installing *source* package ‘seqminer’ ...
** package ‘seqminer’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC = /usr/local/clang18/bin/clang
configure: CFLAGS = -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3
configure: CXX = /usr/local/clang18/bin/clang++ -std=gnu++11
configure: CXXFLAGS = -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3
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 /usr/local/clang18/bin/clang++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... /usr/local/clang18/bin/clang++ -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: ‘clang version 18.1.2’
using C++ compiler: ‘clang version 18.1.2’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/seqminer/src'
have bzip2
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c BGenFile.cpp -o BGenFile.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c BGenIndex.cpp -o BGenIndex.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c BGenVariant.cpp -o BGenVariant.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Exception.cpp -o Exception.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c FileIO.cpp -o FileIO.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c GeneLoader.cpp -o GeneLoader.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c MmapFile.cpp -o MmapFile.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c PatternMatch.cpp -o PatternMatch.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c PeopleSet.cpp -o PeopleSet.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c PlinkInputFile.cpp -o PlinkInputFile.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c PlinkOutputFile.cpp -o PlinkOutputFile.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Profiler.cpp -o Profiler.o
In file included from PlinkOutputFile.cpp:1:
In file included from ./PlinkOutputFile.h:4:
In file included from ./VCFUtil.h:12:
./VCFExtractor.h:65:14: warning: variable 'nMiss' set but not used [-Wunused-but-set-variable]
65 | double nMiss = 0; // number of missing
| ^
1 warning generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c R_CPP_interface.cpp -o R_CPP_interface.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RangeList.cpp -o RangeList.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rannotation.cpp -o Rannotation.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c SimpleMatrix.cpp -o SimpleMatrix.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c SingleChromosomeBCFIndex.cpp -o SingleChromosomeBCFIndex.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c TypeConversion.cpp -o TypeConversion.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Utils.cpp -o Utils.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c VCFHeader.cpp -o VCFHeader.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c VCFIndividual.cpp -o VCFIndividual.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c VCFInfo.cpp -o VCFInfo.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c VCFInputFile.cpp -o VCFInputFile.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_USE_KNETFILE -I. -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c bcf.c -o bcf.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_USE_KNETFILE -I. -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c bcf_index.c -o bcf_index.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_USE_KNETFILE -I. -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -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>:19:1: note: expanded from here
19 | 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>:33:1: note: expanded from here
33 | kh_del_str2id
| ^~~~~~~~~~~~~
2 warnings generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_USE_KNETFILE -I. -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -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>:27:1: note: expanded from here
27 | 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>:41:1: note: expanded from here
41 | kh_del_reg
| ^~~~~~~~~~
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c bgen2genoLoader.cpp -o bgen2genoLoader.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_USE_KNETFILE -I. -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c bgzf.c -o bgzf.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_USE_KNETFILE -I. -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c knetfile.c -o knetfile.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_USE_KNETFILE -I. -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c kstring.c -o kstring.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c plink2genoLoader.cpp -o plink2genoLoader.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c scvcf2genoLoader.cpp -o scvcf2genoLoader.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_USE_KNETFILE -I. -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seqForStat.c -o seqForStat.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_USE_KNETFILE -I. -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seqminer.c -o seqminer.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_USE_KNETFILE -I. -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seqminer_init.c -o seqminer_init.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c tabixLoader.cpp -o tabixLoader.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_USE_KNETFILE -I. -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -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>:38:1: note: expanded from here
38 | 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>:52:1: note: expanded from here
52 | 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>:67:1: note: expanded from here
67 | 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>:81:1: note: expanded from here
81 | kh_del_s
| ^~~~~~~~
6 warnings generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_USE_KNETFILE -I. -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_USE_KNETFILE -I. -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -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
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/seqminer/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/seqminer/src'
have bzip2
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/seqminer/src'
installing to /data/gannet/ripley/R/packages/tests-clang/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)