>>> htslib: Building testing/htslib 1.15.1-r0 (using abuild 3.9.0-r2) started Thu, 14 Jul 2022 12:46:30 +0000 >>> htslib: Checking sanity of /home/buildozer/aports/testing/htslib/APKBUILD... >>> htslib: Analyzing dependencies... >>> htslib: Installing for build: build-base bzip2-dev curl-dev libdeflate-dev xz-dev zlib-dev (1/10) Installing bzip2-dev (1.0.8-r1) (2/10) Installing openssl-dev (1.1.1q-r0) (3/10) Installing nghttp2-dev (1.48.0-r0) (4/10) Installing zlib-dev (1.2.12-r1) (5/10) Installing brotli-dev (1.0.9-r6) (6/10) Installing curl-dev (7.84.0-r0) (7/10) Installing libdeflate (1.10-r0) (8/10) Installing libdeflate-dev (1.10-r0) (9/10) Installing xz-dev (5.2.5-r1) (10/10) Installing .makedepends-htslib (20220714.124632) Executing busybox-1.35.0-r18.trigger OK: 336 MiB in 111 packages >>> htslib: Cleaning up srcdir >>> htslib: Cleaning up pkgdir >>> htslib: Fetching https://distfiles.alpinelinux.org/distfiles/edge/htslib-1.15.1.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 146 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 curl: (22) The requested URL returned error: 404 >>> htslib: Fetching https://github.com/samtools/htslib/releases/download/1.15.1/htslib-1.15.1.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 4044k 100 4044k 0 0 7319k 0 --:--:-- --:--:-- --:--:-- 7319k >>> htslib: Fetching https://distfiles.alpinelinux.org/distfiles/edge/htslib-1.15.1.tar.bz2 >>> htslib: Checking sha512sums... htslib-1.15.1.tar.bz2: OK >>> htslib: Unpacking /var/cache/distfiles/edge/htslib-1.15.1.tar.bz2... checking for x86_64-alpine-linux-musl-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for x86_64-alpine-linux-musl-ranlib... no checking for ranlib... ranlib checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for x86_64-alpine-linux-musl-pkg-config... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for x86_64-alpine-linux-musl... plain .so checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -E checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... 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... no checking for library containing HMAC... -lcrypto checking for library containing regcomp... none required checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk expr: warning: '^\([0-9.]*\)$': using '^' as the first character of a basic regular expression is not portable; it is ignored gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o kfunc.o kfunc.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o kstring.o kstring.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o bgzf.o bgzf.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o errmod.o errmod.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o faidx.o faidx.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o header.o header.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h echo '#define HTS_CC "gcc"' > config_vars.h echo '#define HTS_CPPFLAGS "-Os -fomit-frame-pointer"' >> config_vars.h gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o hts_expr.o hts_expr.c echo '#define HTS_CFLAGS "-Wall -Os -fomit-frame-pointer -fvisibility=hidden"' >> config_vars.h gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o hts_os.o hts_os.c echo '#define HTS_LDFLAGS "-Wl,--as-needed,-O1,--sort-common -fvisibility=hidden "' >> config_vars.h gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o md5.o md5.c echo '#define HTS_LIBS "-ldeflate -llzma -lbz2 -lz -lcurl -lcrypto"' >> config_vars.h gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o multipart.o multipart.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o probaln.o probaln.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o realn.o realn.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o regidx.o regidx.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o region.o region.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o sam.o sam.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o vcf_sweep.o vcf_sweep.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o tbx.o tbx.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o textutils.o textutils.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o thread_pool.o thread_pool.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o vcf.o vcf.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o vcfutils.o vcfutils.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o cram/cram_decode.o cram/cram_decode.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o cram/cram_encode.o cram/cram_encode.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o cram/cram_external.o cram/cram_external.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o cram/cram_index.o cram/cram_index.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o cram/cram_io.o cram/cram_io.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o cram/cram_stats.o cram/cram_stats.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o cram/mFILE.o cram/mFILE.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o cram/string_alloc.o cram/string_alloc.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o hfile_libcurl.o hfile_libcurl.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o hfile_gcs.o hfile_gcs.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o hfile_s3.o hfile_s3.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o hfile_s3_write.o hfile_s3_write.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o kfunc.pico kfunc.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o kstring.pico kstring.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o bgzf.pico bgzf.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o errmod.pico errmod.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o faidx.pico faidx.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o header.pico header.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o hfile.pico hfile.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o hts.pico hts.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o hts_expr.pico hts_expr.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o hts_os.pico hts_os.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o md5.pico md5.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o multipart.pico multipart.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o probaln.pico probaln.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o realn.pico realn.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o regidx.pico regidx.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o region.pico region.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o sam.pico sam.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o tbx.pico tbx.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o textutils.pico textutils.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o thread_pool.pico thread_pool.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o vcf.pico vcf.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o vcfutils.pico vcfutils.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o hfile_libcurl.pico hfile_libcurl.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o hfile_gcs.pico hfile_gcs.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o hfile_s3.pico hfile_s3.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -fpic -c -o hfile_s3_write.pico hfile_s3_write.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o bgzip.o bgzip.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o htsfile.o htsfile.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o tabix.o tabix.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/hts_endian.o test/hts_endian.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/fieldarith.o test/fieldarith.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/hfile.o test/hfile.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/pileup.o test/pileup.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/pileup_mod.o test/pileup_mod.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/sam.o test/sam.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test_bgzf.o test/test_bgzf.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test_expr.o test/test_expr.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test_kfunc.o test/test_kfunc.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test_kstring.o test/test_kstring.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test_mod.o test/test_mod.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test_realn.o test/test_realn.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test-regidx.o test/test-regidx.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test_str2int.o test/test_str2int.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test_view.o test/test_view.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test_index.o test/test_index.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o test/test_introspection.o test/test_introspection.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc gcc -Wall -Os -fomit-frame-pointer -fvisibility=hidden -I. -Os -fomit-frame-pointer -c -o hts.o hts.c gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/hts_endian test/hts_endian.o -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto gcc -shared -Wl,-soname,libhts.so.3 -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico hfile_s3_write.pico -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -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 synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o ln -sf libhts.so libhts.so.3 ranlib libhts.a gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/sam test/sam.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test_expr test/test_expr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test_kfunc test/test_kfunc.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test_mod test/test_mod.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -llzma -lbz2 -lz -lcurl -lcrypto -lpthread >>> htslib: Entering fakeroot... expr: warning: '^\([0-9.]*\)$': using '^' as the first character of a basic regular expression is not portable; it is ignored mkdir -p -m 755 /home/buildozer/aports/testing/htslib/pkg/htslib/usr/bin /home/buildozer/aports/testing/htslib/pkg/htslib/usr/include /home/buildozer/aports/testing/htslib/pkg/htslib/usr/include/htslib /home/buildozer/aports/testing/htslib/pkg/htslib/usr/lib /home/buildozer/aports/testing/htslib/pkg/htslib/usr/share/man/man1 /home/buildozer/aports/testing/htslib/pkg/htslib/usr/share/man/man5 /home/buildozer/aports/testing/htslib/pkg/htslib/usr/share/man/man7 /home/buildozer/aports/testing/htslib/pkg/htslib/usr/lib/pkgconfig if test -n ""; then mkdir -p -m 755 /home/buildozer/aports/testing/htslib/pkg/htslib; fi install -p -m 644 libhts.so /home/buildozer/aports/testing/htslib/pkg/htslib/usr/lib/libhts.so.1.15.1 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib#g;s#@-PACKAGE_VERSION@#1.15.1#g' htslib.pc.tmp > /home/buildozer/aports/testing/htslib/pkg/htslib/usr/lib/pkgconfig/htslib.pc ln -sf libhts.so.1.15.1 /home/buildozer/aports/testing/htslib/pkg/htslib/usr/lib/libhts.so chmod 644 /home/buildozer/aports/testing/htslib/pkg/htslib/usr/lib/pkgconfig/htslib.pc ln -sf libhts.so.1.15.1 /home/buildozer/aports/testing/htslib/pkg/htslib/usr/lib/libhts.so.3 install -p bgzip htsfile tabix /home/buildozer/aports/testing/htslib/pkg/htslib/usr/bin if test -n ""; then install -p /home/buildozer/aports/testing/htslib/pkg/htslib; fi install -p -m 644 htslib/*.h /home/buildozer/aports/testing/htslib/pkg/htslib/usr/include/htslib install -p -m 644 libhts.a /home/buildozer/aports/testing/htslib/pkg/htslib/usr/lib/libhts.a install -p -m 644 bgzip.1 htsfile.1 tabix.1 /home/buildozer/aports/testing/htslib/pkg/htslib/usr/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /home/buildozer/aports/testing/htslib/pkg/htslib/usr/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /home/buildozer/aports/testing/htslib/pkg/htslib/usr/share/man/man7 >>> htslib-static*: Running split function static... >>> htslib-static*: Preparing subpackage htslib-static... >>> htslib-static*: Stripping binaries >>> htslib-static*: Running postcheck for htslib-static >>> htslib-dev*: Running split function dev... >>> htslib-dev*: Preparing subpackage htslib-dev... >>> htslib-dev*: Stripping binaries >>> htslib-dev*: Running postcheck for htslib-dev >>> htslib-tools*: Running split function _tools... '/home/buildozer/aports/testing/htslib/pkg/htslib/usr/bin' -> '/home/buildozer/aports/testing/htslib/pkg/htslib-tools/usr/bin' >>> htslib-tools*: Preparing subpackage htslib-tools... >>> htslib-tools*: Stripping binaries >>> htslib-tools*: Running postcheck for htslib-tools >>> htslib-doc*: Running split function doc... >>> htslib-doc*: Preparing subpackage htslib-doc... >>> htslib-doc*: Running postcheck for htslib-doc >>> htslib*: Running postcheck for htslib >>> htslib*: Preparing package htslib... >>> htslib*: Stripping binaries >>> htslib-dev*: Scanning shared objects >>> htslib-doc*: Scanning shared objects >>> htslib-static*: Scanning shared objects >>> htslib-tools*: Scanning shared objects >>> htslib*: Scanning shared objects >>> htslib-dev*: Tracing dependencies... htslib=1.15.1-r0 pc:liblzma pc:zlib pkgconfig >>> htslib-dev*: Package size: 492.0 KB >>> htslib-dev*: Compressing data... >>> htslib-dev*: Create checksum... >>> htslib-dev*: Create htslib-dev-1.15.1-r0.apk >>> htslib-doc*: Tracing dependencies... >>> htslib-doc*: Package size: 56.0 KB >>> htslib-doc*: Compressing data... >>> htslib-doc*: Create checksum... >>> htslib-doc*: Create htslib-doc-1.15.1-r0.apk >>> htslib-static*: Tracing dependencies... >>> htslib-static*: Package size: 1.1 MB >>> htslib-static*: Compressing data... >>> htslib-static*: Create checksum... >>> htslib-static*: Create htslib-static-1.15.1-r0.apk >>> htslib-tools*: Tracing dependencies... so:libbz2.so.1 so:libc.musl-x86_64.so.1 so:libcrypto.so.1.1 so:libcurl.so.4 so:libdeflate.so.0 so:liblzma.so.5 so:libz.so.1 >>> htslib-tools*: Package size: 1.7 MB >>> htslib-tools*: Compressing data... >>> htslib-tools*: Create checksum... >>> htslib-tools*: Create htslib-tools-1.15.1-r0.apk >>> htslib*: Tracing dependencies... so:libbz2.so.1 so:libc.musl-x86_64.so.1 so:libcrypto.so.1.1 so:libcurl.so.4 so:libdeflate.so.0 so:liblzma.so.5 so:libz.so.1 >>> htslib*: Package size: 696.0 KB >>> htslib*: Compressing data... >>> htslib*: Create checksum... >>> htslib*: Create htslib-1.15.1-r0.apk >>> htslib: Build complete at Thu, 14 Jul 2022 12:46:48 +0000 elapsed time 0h 0m 18s >>> htslib: Cleaning up srcdir >>> htslib: Cleaning up pkgdir >>> htslib: Uninstalling dependencies... (1/10) Purging .makedepends-htslib (20220714.124632) (2/10) Purging bzip2-dev (1.0.8-r1) (3/10) Purging curl-dev (7.84.0-r0) (4/10) Purging nghttp2-dev (1.48.0-r0) (5/10) Purging brotli-dev (1.0.9-r6) (6/10) Purging libdeflate-dev (1.10-r0) (7/10) Purging libdeflate (1.10-r0) (8/10) Purging xz-dev (5.2.5-r1) (9/10) Purging zlib-dev (1.2.12-r1) (10/10) Purging openssl-dev (1.1.1q-r0) Executing busybox-1.35.0-r18.trigger OK: 333 MiB in 101 packages >>> htslib: Updating the testing/x86_64 repository index... >>> htslib: Signing the index...