* installing *source* package 'Rduckhts' ... ** this is package 'Rduckhts' version '0.1.2-0.1.2' ** using staged installation ---------- Checking for required libraries (Windows) ---------- Checking for zlib... zlib: found Checking for bz2... bz2: found INFO: libbz2 found - BZ2 support enabled in htslib Checking for lzma... lzma: found INFO: liblzma found - XZ support enabled in htslib Checking for curl... curl: found INFO: libcurl found - remote URL support enabled in htslib Checking for ssl... ssl: found INFO: OpenSSL found - HTTPS support enabled in htslib Checking for libdeflate... libdeflate: found INFO: libdeflate found - deflate support enabled in htslib Checking for dl... dl: found Checking for gnurx (regex.h, -lgnurx)... gnurx: found ---------- Configuring htslib (Windows) ---------- configure: loading site script /usr/local/etc/config.site checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.exe checking for suffix of executables... .exe 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... 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... /x86_64-w64-mingw32.static.posix/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-MSYS_NT-10.0-20348... MSYS dll checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... x86_64-pc-msys checking host system type... x86_64-pc-msys checking for getpagesize... yes checking for working mmap... no checking for gmtime_r... no checking for fsync... no checking for drand48... no checking for srand48_deterministic... no checking for getauxval... no checking for elf_aux_info... no checking for posix_memalign... no 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 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... no checking for curl_easy_init in -lcurl... no configure: WARNING: libcurl not enabled: library not found configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support configure: WARNING: ref-cache not enabled: unsupported platform 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) ---------- gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o kfunc.o kfunc.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o kstring.o kstring.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o bgzf.o bgzf.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o errmod.o errmod.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o faidx.o faidx.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o header.o header.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -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' \ '-DNDEBUG' \ '-pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden' \ '-fvisibility=hidden ' \ '-ldeflate -llzma -lbz2 -lz -lz -lbz2 -llzma -lcurl -lssl -lcrypto -ldeflate -ldl -lgnurx -lpthread -lws2_32 ' > config_vars.h gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o hts.o hts.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o hts_expr.o hts_expr.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o hts_os.o hts_os.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o md5.o md5.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o multipart.o multipart.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o probaln.o probaln.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o realn.o realn.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o regidx.o regidx.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o region.o region.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o sam.o sam.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o sam_mods.o sam_mods.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o simd.o simd.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o vcf_sweep.o vcf_sweep.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o tbx.o tbx.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o textutils.o textutils.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o thread_pool.o thread_pool.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o vcf.o vcf.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o vcfutils.o vcfutils.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o cram/cram_decode.o cram/cram_decode.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o cram/cram_encode.o cram/cram_encode.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o cram/cram_external.o cram/cram_external.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o cram/cram_index.o cram/cram_index.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o cram/cram_io.o cram/cram_io.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o cram/cram_stats.o cram/cram_stats.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o cram/mFILE.o cram/mFILE.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o cram/string_alloc.o cram/string_alloc.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -mavx2 -mpopcnt -I. -DNDEBUG -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -mavx512f -mpopcnt -I. -DNDEBUG -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I. -DNDEBUG -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -fPIC -D_FILE_OFFSET_BITS=64 -fvisibility=hidden -I. -DNDEBUG -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.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 ranlib libhts.a ---------- Building DuckHTS extension (Windows) ---------- Compiling extension sources for Windows... 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 for Windows... ---------- Cleaning up build artifacts ---------- Appending DuckDB extension metadata... [1] TRUE [1] TRUE ---------- DuckHTS extension built successfully for Windows ---------- -rwxr-xr-x 1 CRANWIN3+CRAN CRANWIN3+Kein 3006820 Feb 13 09:33 /d/temp/2026_02_13_09_30_17_23183/RtmpWIRhvK/R.INSTALL134b025aa2baf/Rduckhts/inst/duckhts_extension/build/duckhts.duckdb_extension Windows 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rduckhts)