* installing *source* package ‘Rduckhts’ ... ** this is package ‘Rduckhts’ version ‘0.1.1-0.0.1’ ** 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... clang-21 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-21 accepts -g... yes checking for clang-21 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... -Wall checking for clang-21 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 clang-21 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... no 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) ---------- clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o kfunc.o kfunc.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o kstring.o kstring.c clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o bgzf.o bgzf.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o errmod.o errmod.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o faidx.o faidx.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o header.o header.c clang-21 -g -O3 -Wall -pedantic -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' \ 'clang-21' \ '-I/usr/local/include -DNDEBUG ' \ '-g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden' \ '-Wl,-O1 -fvisibility=hidden -rdynamic' \ '-ldeflate -llzma -lbz2 -lz -lm -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread' > config_vars.h clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o hts_expr.o hts_expr.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o hts_os.o hts_os.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o md5.o md5.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o multipart.o multipart.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o probaln.o probaln.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o realn.o realn.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o regidx.o regidx.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o region.o region.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o sam.o sam.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o sam_mods.o sam_mods.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o simd.o simd.c clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o vcf_sweep.o vcf_sweep.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o tbx.o tbx.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o textutils.o textutils.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o thread_pool.o thread_pool.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o vcf.o vcf.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o vcfutils.o vcfutils.c clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o cram/mFILE.o cram/mFILE.c clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -DPLUGINPATH=\"/srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/libexec/htslib\" -c -o plugin.o plugin.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o kfunc.pico kfunc.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o kstring.pico kstring.c clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o bgzf.pico bgzf.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o errmod.pico errmod.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o faidx.pico faidx.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o header.pico header.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o hfile.pico hfile.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o hts.pico hts.c clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o md5.pico md5.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o multipart.pico multipart.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o probaln.pico probaln.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o realn.pico realn.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o regidx.pico regidx.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o region.pico region.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o sam.pico sam.c clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o simd.pico simd.c clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o tbx.pico tbx.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o textutils.pico textutils.c clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o vcf.pico vcf.c clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -fpic -c -o vcfutils.pico vcfutils.c clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -DPLUGINPATH=\"/srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/libexec/htslib\" -fpic -c -o plugin.pico plugin.c clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o hts.o hts.c clang-21 -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-O1 -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 -lcurl -lpthread ln -sf libhts.so libhts.so.3 clang-21 -shared -Wl,-E -Wl,-O1 -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 clang-21 -shared -Wl,-E -Wl,-O1 -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 clang-21 -shared -Wl,-E -Wl,-O1 -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 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-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o annot-tsv.o annot-tsv.c clang-21 -Wl,-O1 -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread -lpthread clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o bgzip.o bgzip.c clang-21 -Wl,-O1 -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread -lpthread clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o htsfile.o htsfile.c clang-21 -Wl,-O1 -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread -lpthread clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -I/usr/local/include -DNDEBUG -c -o tabix.o tabix.c clang-21 -Wl,-O1 -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lz -lbz2 -llzma -lcurl -lssl -lcrypto -lpthread -lpthread clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -g -O3 -Wall -pedantic -fpic -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -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 clang-21 -Wl,-O1 -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 mkdir -p -m 755 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/bin /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/include /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/include/htslib /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/lib /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/share/man/man1 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/share/man/man5 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/share/man/man7 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/lib/pkgconfig if test -n "/srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/libexec/htslib"; then mkdir -p -m 755 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/libexec/htslib; fi install -p -m 644 libhts.so /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/lib/libhts.so.1.23 ln -sf libhts.so.1.23 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/lib/libhts.so ln -sf libhts.so.1.23 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/lib/libhts.so.3 sed -e 's#@-includedir@#/srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/include#g;s#@-libdir@#/srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/lib#g;s#@-PACKAGE_VERSION@#1.23#g' htslib.pc.tmp > /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/lib/pkgconfig/htslib.pc chmod 644 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/lib/pkgconfig/htslib.pc install -p annot-tsv bgzip htsfile tabix ref_cache/ref-cache /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/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 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/libexec/htslib; fi install -p -m 644 htslib/*.h /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/include/htslib install -p -m 644 libhts.a /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/lib/libhts.a install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/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 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/share/man/man1 ; \ fi install -p -m 644 faidx.5 sam.5 vcf.5 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/duckhts_extension/htslib/share/man/man7 ---------- Building DuckHTS extension ---------- Compiling extension sources... Compiling duckhts.c -> duckhts.o In file included from duckhts.c:9: In file included from ./duckdb_capi/duckdb_extension.h:18: ./duckdb_capi/duckdb.h:790:64: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 790 | DUCKDB_C_API duckdb_instance_cache duckdb_create_instance_cache(); | ^ | void ./duckdb_capi/duckdb.h:927:48: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 927 | DUCKDB_C_API const char *duckdb_library_version(); | ^ | void ./duckdb_capi/duckdb.h:967:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 967 | DUCKDB_C_API size_t duckdb_config_count(); | ^ | void ./duckdb_capi/duckdb.h:1502:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 1502 | DUCKDB_C_API idx_t duckdb_vector_size(); | ^ | void ./duckdb_capi/duckdb.h:2789:51: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 2789 | DUCKDB_C_API duckdb_value duckdb_create_null_value(); | ^ | void ./duckdb_capi/duckdb.h:3448:66: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3448 | DUCKDB_C_API duckdb_scalar_function duckdb_create_scalar_function(); | ^ | void ./duckdb_capi/duckdb.h:3714:72: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3714 | DUCKDB_C_API duckdb_aggregate_function duckdb_create_aggregate_function(); | ^ | void ./duckdb_capi/duckdb.h:3871:64: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3871 | DUCKDB_C_API duckdb_table_function duckdb_create_table_function(); | ^ | void ./duckdb_capi/duckdb.h:5029:62: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 5029 | DUCKDB_C_API duckdb_cast_function duckdb_create_cast_function(); | ^ | void In file included from duckhts.c:9: ./duckdb_capi/duckdb_extension.h:81:39: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 81 | const char *(*duckdb_library_version)(); | ^ | void ./duckdb_capi/duckdb_extension.h:83:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 83 | size_t (*duckdb_config_count)(); | ^ | void ./duckdb_capi/duckdb_extension.h:100:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 100 | idx_t (*duckdb_vector_size)(); | ^ | void ./duckdb_capi/duckdb_extension.h:238:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 238 | duckdb_value (*duckdb_create_null_value)(); | ^ | void ./duckdb_capi/duckdb_extension.h:300:57: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 300 | duckdb_scalar_function (*duckdb_create_scalar_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:319:63: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 319 | duckdb_aggregate_function (*duckdb_create_aggregate_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:346:55: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 346 | duckdb_table_function (*duckdb_create_table_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:420:53: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 420 | duckdb_cast_function (*duckdb_create_cast_function)(); | ^ | void 17 warnings generated. Compiling bcf_reader.c -> bcf_reader.o In file included from bcf_reader.c:28: In file included from ./duckdb_capi/duckdb_extension.h:18: ./duckdb_capi/duckdb.h:790:64: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 790 | DUCKDB_C_API duckdb_instance_cache duckdb_create_instance_cache(); | ^ | void ./duckdb_capi/duckdb.h:927:48: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 927 | DUCKDB_C_API const char *duckdb_library_version(); | ^ | void ./duckdb_capi/duckdb.h:967:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 967 | DUCKDB_C_API size_t duckdb_config_count(); | ^ | void ./duckdb_capi/duckdb.h:1502:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 1502 | DUCKDB_C_API idx_t duckdb_vector_size(); | ^ | void ./duckdb_capi/duckdb.h:2789:51: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 2789 | DUCKDB_C_API duckdb_value duckdb_create_null_value(); | ^ | void ./duckdb_capi/duckdb.h:3448:66: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3448 | DUCKDB_C_API duckdb_scalar_function duckdb_create_scalar_function(); | ^ | void ./duckdb_capi/duckdb.h:3714:72: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3714 | DUCKDB_C_API duckdb_aggregate_function duckdb_create_aggregate_function(); | ^ | void ./duckdb_capi/duckdb.h:3871:64: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3871 | DUCKDB_C_API duckdb_table_function duckdb_create_table_function(); | ^ | void ./duckdb_capi/duckdb.h:5029:62: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 5029 | DUCKDB_C_API duckdb_cast_function duckdb_create_cast_function(); | ^ | void In file included from bcf_reader.c:28: ./duckdb_capi/duckdb_extension.h:81:39: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 81 | const char *(*duckdb_library_version)(); | ^ | void ./duckdb_capi/duckdb_extension.h:83:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 83 | size_t (*duckdb_config_count)(); | ^ | void ./duckdb_capi/duckdb_extension.h:100:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 100 | idx_t (*duckdb_vector_size)(); | ^ | void ./duckdb_capi/duckdb_extension.h:238:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 238 | duckdb_value (*duckdb_create_null_value)(); | ^ | void ./duckdb_capi/duckdb_extension.h:300:57: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 300 | duckdb_scalar_function (*duckdb_create_scalar_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:319:63: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 319 | duckdb_aggregate_function (*duckdb_create_aggregate_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:346:55: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 346 | duckdb_table_function (*duckdb_create_table_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:420:53: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 420 | duckdb_cast_function (*duckdb_create_cast_function)(); | ^ | void 17 warnings generated. Compiling bam_reader.c -> bam_reader.o In file included from bam_reader.c:21: In file included from ./duckdb_capi/duckdb_extension.h:18: ./duckdb_capi/duckdb.h:790:64: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 790 | DUCKDB_C_API duckdb_instance_cache duckdb_create_instance_cache(); | ^ | void ./duckdb_capi/duckdb.h:927:48: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 927 | DUCKDB_C_API const char *duckdb_library_version(); | ^ | void ./duckdb_capi/duckdb.h:967:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 967 | DUCKDB_C_API size_t duckdb_config_count(); | ^ | void ./duckdb_capi/duckdb.h:1502:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 1502 | DUCKDB_C_API idx_t duckdb_vector_size(); | ^ | void ./duckdb_capi/duckdb.h:2789:51: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 2789 | DUCKDB_C_API duckdb_value duckdb_create_null_value(); | ^ | void ./duckdb_capi/duckdb.h:3448:66: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3448 | DUCKDB_C_API duckdb_scalar_function duckdb_create_scalar_function(); | ^ | void ./duckdb_capi/duckdb.h:3714:72: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3714 | DUCKDB_C_API duckdb_aggregate_function duckdb_create_aggregate_function(); | ^ | void ./duckdb_capi/duckdb.h:3871:64: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3871 | DUCKDB_C_API duckdb_table_function duckdb_create_table_function(); | ^ | void ./duckdb_capi/duckdb.h:5029:62: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 5029 | DUCKDB_C_API duckdb_cast_function duckdb_create_cast_function(); | ^ | void In file included from bam_reader.c:21: ./duckdb_capi/duckdb_extension.h:81:39: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 81 | const char *(*duckdb_library_version)(); | ^ | void ./duckdb_capi/duckdb_extension.h:83:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 83 | size_t (*duckdb_config_count)(); | ^ | void ./duckdb_capi/duckdb_extension.h:100:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 100 | idx_t (*duckdb_vector_size)(); | ^ | void ./duckdb_capi/duckdb_extension.h:238:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 238 | duckdb_value (*duckdb_create_null_value)(); | ^ | void ./duckdb_capi/duckdb_extension.h:300:57: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 300 | duckdb_scalar_function (*duckdb_create_scalar_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:319:63: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 319 | duckdb_aggregate_function (*duckdb_create_aggregate_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:346:55: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 346 | duckdb_table_function (*duckdb_create_table_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:420:53: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 420 | duckdb_cast_function (*duckdb_create_cast_function)(); | ^ | void 17 warnings generated. Compiling seq_reader.c -> seq_reader.o In file included from seq_reader.c:22: In file included from ./duckdb_capi/duckdb_extension.h:18: ./duckdb_capi/duckdb.h:790:64: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 790 | DUCKDB_C_API duckdb_instance_cache duckdb_create_instance_cache(); | ^ | void ./duckdb_capi/duckdb.h:927:48: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 927 | DUCKDB_C_API const char *duckdb_library_version(); | ^ | void ./duckdb_capi/duckdb.h:967:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 967 | DUCKDB_C_API size_t duckdb_config_count(); | ^ | void ./duckdb_capi/duckdb.h:1502:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 1502 | DUCKDB_C_API idx_t duckdb_vector_size(); | ^ | void ./duckdb_capi/duckdb.h:2789:51: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 2789 | DUCKDB_C_API duckdb_value duckdb_create_null_value(); | ^ | void ./duckdb_capi/duckdb.h:3448:66: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3448 | DUCKDB_C_API duckdb_scalar_function duckdb_create_scalar_function(); | ^ | void ./duckdb_capi/duckdb.h:3714:72: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3714 | DUCKDB_C_API duckdb_aggregate_function duckdb_create_aggregate_function(); | ^ | void ./duckdb_capi/duckdb.h:3871:64: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3871 | DUCKDB_C_API duckdb_table_function duckdb_create_table_function(); | ^ | void ./duckdb_capi/duckdb.h:5029:62: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 5029 | DUCKDB_C_API duckdb_cast_function duckdb_create_cast_function(); | ^ | void In file included from seq_reader.c:22: ./duckdb_capi/duckdb_extension.h:81:39: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 81 | const char *(*duckdb_library_version)(); | ^ | void ./duckdb_capi/duckdb_extension.h:83:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 83 | size_t (*duckdb_config_count)(); | ^ | void ./duckdb_capi/duckdb_extension.h:100:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 100 | idx_t (*duckdb_vector_size)(); | ^ | void ./duckdb_capi/duckdb_extension.h:238:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 238 | duckdb_value (*duckdb_create_null_value)(); | ^ | void ./duckdb_capi/duckdb_extension.h:300:57: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 300 | duckdb_scalar_function (*duckdb_create_scalar_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:319:63: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 319 | duckdb_aggregate_function (*duckdb_create_aggregate_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:346:55: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 346 | duckdb_table_function (*duckdb_create_table_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:420:53: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 420 | duckdb_cast_function (*duckdb_create_cast_function)(); | ^ | void 17 warnings generated. Compiling tabix_reader.c -> tabix_reader.o In file included from tabix_reader.c:29: In file included from ./duckdb_capi/duckdb_extension.h:18: ./duckdb_capi/duckdb.h:790:64: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 790 | DUCKDB_C_API duckdb_instance_cache duckdb_create_instance_cache(); | ^ | void ./duckdb_capi/duckdb.h:927:48: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 927 | DUCKDB_C_API const char *duckdb_library_version(); | ^ | void ./duckdb_capi/duckdb.h:967:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 967 | DUCKDB_C_API size_t duckdb_config_count(); | ^ | void ./duckdb_capi/duckdb.h:1502:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 1502 | DUCKDB_C_API idx_t duckdb_vector_size(); | ^ | void ./duckdb_capi/duckdb.h:2789:51: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 2789 | DUCKDB_C_API duckdb_value duckdb_create_null_value(); | ^ | void ./duckdb_capi/duckdb.h:3448:66: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3448 | DUCKDB_C_API duckdb_scalar_function duckdb_create_scalar_function(); | ^ | void ./duckdb_capi/duckdb.h:3714:72: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3714 | DUCKDB_C_API duckdb_aggregate_function duckdb_create_aggregate_function(); | ^ | void ./duckdb_capi/duckdb.h:3871:64: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 3871 | DUCKDB_C_API duckdb_table_function duckdb_create_table_function(); | ^ | void ./duckdb_capi/duckdb.h:5029:62: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 5029 | DUCKDB_C_API duckdb_cast_function duckdb_create_cast_function(); | ^ | void In file included from tabix_reader.c:29: ./duckdb_capi/duckdb_extension.h:81:39: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 81 | const char *(*duckdb_library_version)(); | ^ | void ./duckdb_capi/duckdb_extension.h:83:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 83 | size_t (*duckdb_config_count)(); | ^ | void ./duckdb_capi/duckdb_extension.h:100:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 100 | idx_t (*duckdb_vector_size)(); | ^ | void ./duckdb_capi/duckdb_extension.h:238:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 238 | duckdb_value (*duckdb_create_null_value)(); | ^ | void ./duckdb_capi/duckdb_extension.h:300:57: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 300 | duckdb_scalar_function (*duckdb_create_scalar_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:319:63: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 319 | duckdb_aggregate_function (*duckdb_create_aggregate_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:346:55: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 346 | duckdb_table_function (*duckdb_create_table_function)(); | ^ | void ./duckdb_capi/duckdb_extension.h:420:53: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 420 | duckdb_cast_function (*duckdb_create_cast_function)(); | ^ | void 17 warnings generated. 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 ---------- -rwxrwxr-x 1 hornik hornik 224654 Feb 9 21:43 /srv/hornik/tmp/CRAN_pretest/Rduckhts.Rcheck/00_pkg_src/Rduckhts/inst/extdata/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)