Install log for 'Rduckhts'

* installing *source* package ‘Rduckhts’ ...
** this is package ‘Rduckhts’ version ‘0.1.2-0.1.4’
** package ‘Rduckhts’ successfully unpacked and MD5 sums checked
** using staged installation
---------- Checking for required headers and libraries ----------
Checking for zlib (zlib.h, -lz)...
  zlib: found
Checking for bz2 (bzlib.h, -lbz2)...
  bz2: found
Checking for lzma (lzma.h, -llzma)...
  lzma: found
Checking for curl (curl/curl.h, -lcurl)...
  curl: found
Checking for openssl (openssl/ssl.h, -lssl -lcrypto)...
  openssl: found
---------- Configuring htslib ----------
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for ranlib... gcc-ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for gcc options needed to detect all undeclared functions... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/param.h... yes
checking whether _XOPEN_SOURCE is declared... no
checking whether __get_cpuid_max is declared... yes
checking whether __cpuid_count is declared... yes
checking for x86intrin.h... yes
checking C compiler flags needed for sse4.1... -msse4.1 -mssse3 -mpopcnt
checking C compiler flags needed for avx2... -mavx2 -mpopcnt
checking C compiler flags needed for avx512f... -mavx512f -mpopcnt
checking for working __builtin_cpu_supports("ssse3")... yes
checking for working __attribute__((target("ssse3")))... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for gcc option to enable large file support... none needed
checking shared library type for unknown-Linux... plain .so
checking whether the linker supports versioned symbols... yes
checking whether the compiler accepts -fvisibility=hidden... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
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 for getauxval... yes
checking for elf_aux_info... no
checking for posix_memalign... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for __attribute__((constructor))... yes
checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes
checking for library containing dlsym... none required
checking whether the compiler accepts -rdynamic... 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 for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking whether htscodecs files are present... yes
checking for libdeflate.h... yes
checking for libdeflate_deflate_compress in -ldeflate... yes
checking for curl/curl.h... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... none required
checking for fstatat... yes
checking for CMSG_LEN... yes
checking for epoll... yes (edge triggered)
checking for sendfile... yes, Linux-style
checking whether EHOSTDOWN is declared... yes
checking whether ENONET is declared... yes
checking whether AI_V4MAPPED is declared... yes
checking whether AI_ADDRCONFIG is declared... yes
checking whether the compiler accepts -Wextra... yes
checking whether the compiler accepts -Wformat... yes
checking whether the compiler accepts -Wformat=2... yes
checking whether the compiler accepts -Wconversion... yes
checking whether the compiler accepts -Wtrampolines... yes
checking whether the compiler accepts -Wstrict-aliasing... yes
checking whether the compiler accepts -fstack-clash-protection... yes
checking whether the compiler accepts -fstack-protector-strong... yes
checking whether the compiler accepts -fcf-protection=full... yes
checking whether the compiler accepts -mbranch-protection=standard... no
checking whether the compiler accepts -fno-delete-null-pointer-checks... yes
checking whether the compiler accepts -Wl,-z,noexecstack... yes
checking whether the compiler accepts -Wl,-z,relro... yes
checking whether the compiler accepts -Wl,-z,now... yes
checking whether the compiler accepts -Wl,--as-needed... yes
checking whether the compiler accepts -Wl,--no-copy-dt-needed-entries... yes
checking whether the compiler accepts -Wl,-z,nodlopen... yes
checking for library containing regcomp... none required
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
---------- Building htslib (static + shared) ----------
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib'
make[1]: warning: -j1 forced in submake: resetting jobserver mode.
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o kfunc.o kfunc.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o kstring.o kstring.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o bgzf.o bgzf.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o errmod.o errmod.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o faidx.o faidx.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o header.o header.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.23"' > version.h
printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \
'gcc' \
'-I/usr/local/include -DNDEBUG ' \
'-g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden' \
'-L/usr/local/lib64 -fvisibility=hidden -rdynamic' \
'-ldeflate -llzma -lbz2 -lz -lm  -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread' > config_vars.h
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o hts.o hts.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o hts_expr.o hts_expr.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o hts_os.o hts_os.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o md5.o md5.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o multipart.o multipart.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o probaln.o probaln.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o realn.o realn.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o regidx.o regidx.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o region.o region.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o sam.o sam.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o sam_mods.o sam_mods.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o simd.o simd.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o tbx.o tbx.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o textutils.o textutils.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o thread_pool.o thread_pool.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o vcf.o vcf.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o vcfutils.o vcfutils.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -mavx2 -mpopcnt -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -mavx512f -mpopcnt -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -DPLUGINPATH=\"/data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/libexec/htslib\" -c -o plugin.o plugin.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 sam_mods.o simd.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_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o  plugin.o
gcc-ranlib libhts.a
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o kfunc.pico kfunc.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o kstring.pico kstring.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o bgzf.pico bgzf.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o errmod.pico errmod.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o faidx.pico faidx.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o header.pico header.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o hfile.pico hfile.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o hts.pico hts.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o hts_expr.pico hts_expr.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o hts_os.pico hts_os.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o md5.pico md5.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o multipart.pico multipart.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o probaln.pico probaln.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o realn.pico realn.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o regidx.pico regidx.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o region.pico region.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o sam.pico sam.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o sam_mods.pico sam_mods.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o simd.pico simd.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o tbx.pico tbx.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o textutils.pico textutils.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o thread_pool.pico thread_pool.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o vcf.pico vcf.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o vcfutils.pico vcfutils.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -mavx2 -mpopcnt -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -mavx512f -mpopcnt -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -DPLUGINPATH=\"/data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/libexec/htslib\" -fpic -c -o plugin.pico plugin.c
gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -L/usr/local/lib64 -fvisibility=hidden -rdynamic -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 sam_mods.pico simd.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_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.pico plugin.pico -ldeflate -llzma -lbz2 -lz -lm  -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread -lpthread
ln -sf libhts.so libhts.so.3
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -shared -Wl,-E -L/usr/local/lib64 -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -llzma -lbz2 -lz -lm  -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread -lcurl -lpthread
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o hfile_gcs.pico hfile_gcs.c
gcc -shared -Wl,-E -L/usr/local/lib64 -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -llzma -lbz2 -lz -lm  -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread -lpthread
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -fpic -c -o hfile_s3.pico hfile_s3.c
gcc -shared -Wl,-E -L/usr/local/lib64 -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -llzma -lbz2 -lz -lm  -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread  -lcurl -lpthread
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib'
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o annot-tsv.o annot-tsv.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o bgzip.o bgzip.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o htsfile.o htsfile.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden  -I. -I/usr/local/include -DNDEBUG  -c -o tabix.o tabix.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/cmsg_wrap.o ref_cache/cmsg_wrap.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/http_parser.o ref_cache/http_parser.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/listener.o ref_cache/listener.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/log_files.o ref_cache/log_files.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/main.o ref_cache/main.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/misc.o ref_cache/misc.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/ping.o ref_cache/ping.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_epoll.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/poll_wrap_poll.o ref_cache/poll_wrap_poll.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/ref_files.o ref_cache/ref_files.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/request_handler.o ref_cache/request_handler.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/sendfile_wrap.o ref_cache/sendfile_wrap.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/server.o ref_cache/server.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/transaction.o ref_cache/transaction.c
gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I. -I/usr/local/include -DNDEBUG  -c -o ref_cache/upstream.o ref_cache/upstream.c
mkdir -p -m 755 /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/bin /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/include /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/include/htslib /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/lib /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/share/man/man1 /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/share/man/man5 /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/share/man/man7 /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/lib/pkgconfig
if test -n "/data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/libexec/htslib"; then mkdir -p -m 755 /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/libexec/htslib; fi
gcc -L/usr/local/lib64 -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -ldeflate -llzma -lbz2 -lz -lm  -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread -lpthread
gcc -L/usr/local/lib64 -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm  -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread -lpthread
gcc -L/usr/local/lib64 -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm  -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread -lpthread
gcc -L/usr/local/lib64 -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm  -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread -lpthread
gcc -L/usr/local/lib64 -fvisibility=hidden -rdynamic -Wl,-z,noexecstack -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,nodlopen -o ref_cache/ref-cache ref_cache/cmsg_wrap.o ref_cache/http_parser.o ref_cache/listener.o ref_cache/log_files.o ref_cache/main.o ref_cache/misc.o ref_cache/ping.o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_poll.o ref_cache/ref_files.o ref_cache/request_handler.o ref_cache/sendfile_wrap.o ref_cache/server.o ref_cache/transaction.o ref_cache/upstream.o cram/pooled_alloc.o md5.o -lcurl
install -p -m 644 libhts.so /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/lib/libhts.so.1.23
ln -sf libhts.so.1.23 /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/lib/libhts.so
ln -sf libhts.so.1.23 /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/lib/libhts.so.3
sed -e 's#@-includedir@#/data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/include#g;s#@-libdir@#/data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/lib#g;s#@-PACKAGE_VERSION@#1.23#g' htslib.pc.tmp > /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/lib/pkgconfig/htslib.pc
chmod 644 /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/lib/pkgconfig/htslib.pc
install -p annot-tsv bgzip htsfile tabix ref_cache/ref-cache /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/bin
if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so"; then install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/libexec/htslib; fi
install -p -m 644 htslib/*.h /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/include/htslib
install -p -m 644 libhts.a /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/lib/libhts.a
install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/share/man/man1
if test "xref_cache/ref-cache" != "x" ; then \
    install -p -m 644 ref_cache/ref-cache.1 /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/share/man/man1 ; \
fi
install -p -m 644 faidx.5 sam.5 vcf.5 /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/share/man/man5
install -p -m 644 htslib-s3-plugin.7 /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib/share/man/man7
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/htslib'
---------- Building DuckHTS extension ----------
Compiling extension sources...
  Compiling duckhts.c -> duckhts.o
  Compiling bcf_reader.c -> bcf_reader.o
  Compiling bam_reader.c -> bam_reader.o
  Compiling seq_reader.c -> seq_reader.o
  Compiling tabix_reader.c -> tabix_reader.o
  Compiling vep_parser.c -> vep_parser.o
Linking DuckHTS extension...
---------- Cleaning up build artifacts ----------
Appending DuckDB extension metadata...
[1] TRUE
[1] TRUE
---------- DuckHTS extension built successfully ----------
-rwxr-xr-x 1 ripley bdr 356494 Feb 23 19:02 /data/gannet/ripley/R/packages/tests-devel/Rduckhts/inst/duckhts_extension/build/duckhts.duckdb_extension
Configure complete
** R
** 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 (Rduckhts)