some errors when do "make"

[gaom001]

lumpy-sv-0.3.1 gaom4$ make cd lib/htslib && \ ./configure --disable-bz2 --disable-lzma --enable-libcurl checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -E 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 stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for library containing regcomp... none required checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk CFLAGS=" -DBGZF" make -C lib/htslib --no-print-directory CFLAGS="-DBGZF_MT" gcc -DBGZF_MT -I. -c -o kfunc.o kfunc.c gcc -DBGZF_MT -I. -c -o kstring.o kstring.c gcc -DBGZF_MT -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -DBGZF_MT -I. -c -o bgzf.o bgzf.c bgzf.c:57:0: warning: "BGZF_MT" redefined [enabled by default]

define BGZF_MT

^

:0:0: note: this is the location of the previous definition gcc -DBGZF_MT -I. -c -o errmod.o errmod.c gcc -DBGZF_MT -I. -c -o faidx.o faidx.c gcc -DBGZF_MT -I. -c -o header.o header.c gcc -DBGZF_MT -I. -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.15"' > version.h echo '#define HTS_CC "gcc"' > config_vars.h echo '#define HTS_CPPFLAGS ""' >> config_vars.h echo '#define HTS_CFLAGS "-DBGZF_MT"' >> config_vars.h echo '#define HTS_LDFLAGS "-fvisibility=hidden "' >> config_vars.h echo '#define HTS_LIBS "-lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto"' >> config_vars.h gcc -DBGZF_MT -I. -c -o hts.o hts.c gcc -DBGZF_MT -I. -c -o hts_expr.o hts_expr.c gcc -DBGZF_MT -I. -c -o hts_os.o hts_os.c gcc -DBGZF_MT -I. -c -o md5.o md5.c gcc -DBGZF_MT -I. -c -o multipart.o multipart.c gcc -DBGZF_MT -I. -c -o probaln.o probaln.c gcc -DBGZF_MT -I. -c -o realn.o realn.c gcc -DBGZF_MT -I. -c -o regidx.o regidx.c gcc -DBGZF_MT -I. -c -o region.o region.c gcc -DBGZF_MT -I. -c -o sam.o sam.c gcc -DBGZF_MT -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -DBGZF_MT -I. -c -o vcf_sweep.o vcf_sweep.c gcc -DBGZF_MT -I. -c -o tbx.o tbx.c gcc -DBGZF_MT -I. -c -o textutils.o textutils.c gcc -DBGZF_MT -I. -c -o thread_pool.o thread_pool.c gcc -DBGZF_MT -I. -c -o vcf.o vcf.c gcc -DBGZF_MT -I. -c -o vcfutils.o vcfutils.c gcc -DBGZF_MT -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -DBGZF_MT -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -DBGZF_MT -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -DBGZF_MT -I. -c -o cram/cram_external.o cram/cram_external.c gcc -DBGZF_MT -I. -c -o cram/cram_index.o cram/cram_index.c gcc -DBGZF_MT -I. -c -o cram/cram_io.o cram/cram_io.c gcc -DBGZF_MT -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -DBGZF_MT -I. -c -o cram/mFILE.o cram/mFILE.c gcc -DBGZF_MT -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -DBGZF_MT -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -DBGZF_MT -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -DBGZF_MT -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -DBGZF_MT -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -DBGZF_MT -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -DBGZF_MT -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -DBGZF_MT -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -DBGZF_MT -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -DBGZF_MT -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -DBGZF_MT -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -DBGZF_MT -I. -c -o hfile_libcurl.o hfile_libcurl.c gcc -DBGZF_MT -I. -c -o hfile_gcs.o hfile_gcs.c gcc -DBGZF_MT -I. -c -o hfile_s3.o hfile_s3.c gcc -DBGZF_MT -I. -c -o hfile_s3_write.o hfile_s3_write.c ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o ranlib libhts.a gcc -DBGZF_MT -I. -fpic -c -o kfunc.pico kfunc.c gcc -DBGZF_MT -I. -fpic -c -o kstring.pico kstring.c gcc -DBGZF_MT -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -DBGZF_MT -I. -fpic -c -o bgzf.pico bgzf.c bgzf.c:57:0: warning: "BGZF_MT" redefined [enabled by default] #define BGZF_MT ^ :0:0: note: this is the location of the previous definition gcc -DBGZF_MT -I. -fpic -c -o errmod.pico errmod.c gcc -DBGZF_MT -I. -fpic -c -o faidx.pico faidx.c gcc -DBGZF_MT -I. -fpic -c -o header.pico header.c gcc -DBGZF_MT -I. -fpic -c -o hfile.pico hfile.c gcc -DBGZF_MT -I. -fpic -c -o hts.pico hts.c gcc -DBGZF_MT -I. -fpic -c -o hts_expr.pico hts_expr.c gcc -DBGZF_MT -I. -fpic -c -o hts_os.pico hts_os.c gcc -DBGZF_MT -I. -fpic -c -o md5.pico md5.c gcc -DBGZF_MT -I. -fpic -c -o multipart.pico multipart.c gcc -DBGZF_MT -I. -fpic -c -o probaln.pico probaln.c gcc -DBGZF_MT -I. -fpic -c -o realn.pico realn.c gcc -DBGZF_MT -I. -fpic -c -o regidx.pico regidx.c gcc -DBGZF_MT -I. -fpic -c -o region.pico region.c gcc -DBGZF_MT -I. -fpic -c -o sam.pico sam.c gcc -DBGZF_MT -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -DBGZF_MT -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -DBGZF_MT -I. -fpic -c -o tbx.pico tbx.c gcc -DBGZF_MT -I. -fpic -c -o textutils.pico textutils.c gcc -DBGZF_MT -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -DBGZF_MT -I. -fpic -c -o vcf.pico vcf.c gcc -DBGZF_MT -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -DBGZF_MT -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -DBGZF_MT -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -DBGZF_MT -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -DBGZF_MT -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -DBGZF_MT -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -DBGZF_MT -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -DBGZF_MT -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -DBGZF_MT -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -DBGZF_MT -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -DBGZF_MT -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -DBGZF_MT -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -DBGZF_MT -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c gcc -DBGZF_MT -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c gcc -DBGZF_MT -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c gcc -DBGZF_MT -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c gcc -DBGZF_MT -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c gcc -DBGZF_MT -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c gcc -DBGZF_MT -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c gcc -DBGZF_MT -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c gcc -DBGZF_MT -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c gcc -DBGZF_MT -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c gcc -DBGZF_MT -I. -fpic -c -o hfile_s3.pico hfile_s3.c gcc -DBGZF_MT -I. -fpic -c -o hfile_s3_write.pico hfile_s3_write.c gcc -shared -Wl,-soname,libhts.so.3 -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico hfile_s3_write.pico -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread ln -sf libhts.so libhts.so.3 gcc -DBGZF_MT -I. -c -o bgzip.o bgzip.c gcc -fvisibility=hidden -o bgzip bgzip.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o htsfile.o htsfile.c gcc -fvisibility=hidden -o htsfile htsfile.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o tabix.o tabix.c gcc -fvisibility=hidden -o tabix tabix.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/hts_endian.o test/hts_endian.c gcc -fvisibility=hidden -o test/hts_endian test/hts_endian.o -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto gcc -DBGZF_MT -I. -c -o test/fieldarith.o test/fieldarith.c gcc -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/hfile.o test/hfile.c gcc -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/pileup.o test/pileup.c gcc -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/pileup_mod.o test/pileup_mod.c gcc -fvisibility=hidden -o test/pileup_mod test/pileup_mod.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -fvisibility=hidden -o test/plugins-dlhts test/plugins-dlhts.o -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto gcc -DBGZF_MT -I. -c -o test/sam.o test/sam.c gcc -fvisibility=hidden -o test/sam test/sam.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test_expr.o test/test_expr.c gcc -fvisibility=hidden -o test/test_expr test/test_expr.o libhts.a -lz -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test_kfunc.o test/test_kfunc.c gcc -fvisibility=hidden -o test/test_kfunc test/test_kfunc.o libhts.a -lz -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test_kstring.o test/test_kstring.c gcc -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test_mod.o test/test_mod.c gcc -fvisibility=hidden -o test/test_mod test/test_mod.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test_realn.o test/test_realn.c gcc -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test-regidx.o test/test-regidx.c gcc -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test_str2int.o test/test_str2int.c gcc -fvisibility=hidden -o test/test_str2int test/test_str2int.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test_view.o test/test_view.c gcc -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test_index.o test/test_index.c gcc -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -DBGZF_MT -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread gcc -DBGZF_MT -I. -c -o test/test_introspection.o test/test_introspection.c gcc -fvisibility=hidden -o test/test_introspection test/test_introspection.o libhts.a -lz -lm -lz -L /home/gaom4/src/zlib-1.2.8 -lcurl -lcrypto -lpthread sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc [ -d bin ] || mkdir -p bin make --no-print-directory -C src/filter/ cc -I../../lib/htslib/ -o lumpy_filter filter.c ../../lib/htslib/libhts.a -lcrypto -lcurl -lpthread -lz ../../lib/htslib/libhts.a(fqzcomp_qual.o): In function `fqz_qual_stats': fqzcomp_qual.c:(.text+0x27f1): undefined reference to `log' fqzcomp_qual.c:(.text+0x287e): undefined reference to `log' fqzcomp_qual.c:(.text+0x2925): undefined reference to `log' fqzcomp_qual.c:(.text+0x29b2): undefined reference to `log' fqzcomp_qual.c:(.text+0x2a59): undefined reference to `log' ../../lib/htslib/libhts.a(fqzcomp_qual.o):fqzcomp_qual.c:(.text+0x2b02): more undefined references to `log' follow collect2: error: ld returned 1 exit status make[1]: *** [all] Error 1 make: *** [lumpy_filter] Error 2

[gaom001]

Do not know what causes these two errors, please advise.