* installing *source* package ‘Rduckhts’ ...
** this is package ‘Rduckhts’ version ‘0.1.3-0.0.2’
** 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, -L/opt/R/x86_64/lib -lssl -lcrypto)...
openssl: found
---------- Configuring htslib ----------
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to enable C11 features... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... rm: conftest.dSYM: is a directory
-Wall
checking for clang 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... /opt/R/x86_64/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for clang option to enable large file support... none needed
checking shared library type for unknown-Darwin... Darwin dylib
checking whether the compiler accepts -fvisibility=hidden... yes
checking build system type... x86_64-apple-darwin22.4.0
checking host system type... x86_64-apple-darwin22.4.0
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... no
checking for elf_aux_info... no
checking for posix_memalign... yes
checking whether fdatasync is declared... no
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... none required
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... yes
checking for fstatat... yes
checking for CMSG_LEN... yes
checking for epoll... no
checking for sendfile... yes, macOS-style
checking whether EHOSTDOWN is declared... no
checking whether ENONET is declared... no
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... no
checking whether the compiler accepts -Wstrict-aliasing... yes
checking whether the compiler accepts -fstack-clash-protection... no
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... no
checking whether the compiler accepts -Wl,-z,relro... no
checking whether the compiler accepts -Wl,-z,now... no
checking whether the compiler accepts -Wl,--as-needed... no
checking whether the compiler accepts -Wl,--no-copy-dt-needed-entries... no
checking whether the compiler accepts -Wl,-z,nodlopen... no
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) ----------
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o kfunc.o kfunc.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o kstring.o kstring.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o bcf_sr_sort.o bcf_sr_sort.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o bgzf.o bgzf.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o errmod.o errmod.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o faidx.o faidx.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o header.o header.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -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' \
'clang' \
'-I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include' \
'-falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden' \
'-L/opt/R/x86_64/lib -fvisibility=hidden -rdynamic' \
'-ldeflate -llzma -lbz2 -lz -lz -lbz2 -llzma -lcurl -L/opt/R/x86_64/lib -lssl -lcrypto -lpthread' > config_vars.h
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o hts.o hts.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o hts_expr.o hts_expr.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o hts_os.o hts_os.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o md5.o md5.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o multipart.o multipart.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o probaln.o probaln.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o realn.o realn.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o regidx.o regidx.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o region.o region.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o sam.o sam.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o sam_mods.o sam_mods.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o simd.o simd.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o synced_bcf_reader.o synced_bcf_reader.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o vcf_sweep.o vcf_sweep.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o tbx.o tbx.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o textutils.o textutils.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o thread_pool.o thread_pool.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o vcf.o vcf.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o vcfutils.o vcfutils.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o cram/cram_codecs.o cram/cram_codecs.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o cram/cram_decode.o cram/cram_decode.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o cram/cram_encode.o cram/cram_encode.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o cram/cram_external.o cram/cram_external.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o cram/cram_index.o cram/cram_index.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o cram/cram_io.o cram/cram_io.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o cram/cram_stats.o cram/cram_stats.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o cram/mFILE.o cram/mFILE.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o cram/open_trace_file.o cram/open_trace_file.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o cram/pooled_alloc.o cram/pooled_alloc.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o cram/string_alloc.o cram/string_alloc.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -mavx2 -mpopcnt -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -mavx512f -mpopcnt -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -DPLUGINPATH=\"/Volumes/Builds/packages/big-sur-x86_64/results/4.5/Rduckhts.Rcheck/00_pkg_src/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
ranlib libhts.a
clang -dynamiclib -install_name /Volumes/Builds/packages/big-sur-x86_64/results/4.5/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/lib/libhts.3.dylib -current_version 3.1.23 -compatibility_version 3.1.23 -L/opt/R/x86_64/lib -fvisibility=hidden -rdynamic -o libhts.dylib 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 -ldeflate -llzma -lbz2 -lz -lz -lbz2 -llzma -lcurl -L/opt/R/x86_64/lib -lssl -lcrypto -lpthread
ln -sf libhts.dylib libhts.3.dylib
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o hfile_libcurl.o hfile_libcurl.c
clang -bundle -Wl,-undefined,dynamic_lookup -L/opt/R/x86_64/lib -fvisibility=hidden -rdynamic -o hfile_libcurl.bundle hfile_libcurl.o -ldeflate -llzma -lbz2 -lz -lz -lbz2 -llzma -lcurl -L/opt/R/x86_64/lib -lssl -lcrypto -lpthread -lcurl
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o hfile_gcs.o hfile_gcs.c
clang -bundle -Wl,-undefined,dynamic_lookup -L/opt/R/x86_64/lib -fvisibility=hidden -rdynamic -o hfile_gcs.bundle hfile_gcs.o -ldeflate -llzma -lbz2 -lz -lz -lbz2 -llzma -lcurl -L/opt/R/x86_64/lib -lssl -lcrypto -lpthread
clang -falign-functions=64 -Wall -g -O2 -fPIC -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/opt/R/x86_64/include -DNDEBUG -I/opt/R/x86_64/include -c -o hfile_s3.o hfile_s3.c
clang -bundle -Wl,-undefined,dynamic_lookup -L/opt/R/x86_64/lib -fvisibility=hidden -rdynamic -o hfile_s3.bundle hfile_s3.o -ldeflate -llzma -lbz2 -lz -lz -lbz2 -llzma -lcurl -L/opt/R/x86_64/lib -lssl -lcrypto -lpthread -lcurl
Fixing htslib install names for macOS...
---------- 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 hts_meta_reader.c -> hts_meta_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 urbanek staff 134510 Feb 25 08:36 /Volumes/Builds/packages/big-sur-x86_64/results/4.5/Rduckhts.Rcheck/00_pkg_src/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)