>>> htslib: Building testing/htslib 1.19-r0 (using abuild 3.12.0-r0) started Tue, 12 Dec 2023 17:44:09 +0000
>>> htslib: Checking sanity of /home/buildozer/aports/testing/htslib/APKBUILD...
>>> WARNING: htslib: No maintainer
>>> htslib: Analyzing dependencies...
>>> htslib: Installing for build: build-base bzip2-dev curl-dev libdeflate-dev xz-dev zlib-dev
(1/16) Installing libbz2 (1.0.8-r6)
(2/16) Installing bzip2-dev (1.0.8-r6)
(3/16) Installing brotli (1.1.0-r1)
(4/16) Installing brotli-dev (1.1.0-r1)
(5/16) Installing c-ares-dev (1.23.0-r0)
(6/16) Installing libidn2-dev (2.3.4-r4)
(7/16) Installing nghttp2-dev (1.58.0-r0)
(8/16) Installing openssl-dev (3.1.4-r2)
(9/16) Installing zlib-dev (1.3-r2)
(10/16) Installing curl-dev (8.5.0-r0)
(11/16) Installing libdeflate (1.19-r0)
(12/16) Installing libdeflate-dev (1.19-r0)
(13/16) Installing xz-libs (5.4.5-r0)
(14/16) Installing xz (5.4.5-r0)
(15/16) Installing xz-dev (5.4.5-r0)
(16/16) Installing .makedepends-htslib (20231212.174410)
Executing busybox-1.36.1-r16.trigger
OK: 274 MiB in 120 packages
>>> htslib: Cleaning up srcdir
>>> htslib: Cleaning up pkgdir
>>> htslib: Cleaning up tmpdir
>>> htslib: Fetching https://distfiles.alpinelinux.org/distfiles/edge/htslib-1.19.tar.bz2
>>> htslib: Fetching https://distfiles.alpinelinux.org/distfiles/edge/htslib-1.19.tar.bz2
>>> htslib: Checking sha512sums...
htslib-1.19.tar.bz2: OK
>>> htslib: Unpacking /var/cache/distfiles/htslib-1.19.tar.bz2...
checking for armv7-alpine-linux-musleabihf-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for armv7-alpine-linux-musleabihf-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 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... yes
checking C compiler flags needed for sse4.1... none
checking C compiler flags needed for avx2... none
checking C compiler flags needed for avx512f... none
checking for armv7-alpine-linux-musleabihf-pkg-config... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for gcc option to enable large file support... none needed
checking shared library type for armv7-alpine-linux-musleabihf... plain .so
checking whether the linker supports versioned symbols... yes
checking whether the compiler accepts -fvisibility=hidden... yes
checking build system type... armv7-alpine-linux-musleabihf
checking host system type... armv7-alpine-linux-musleabihf
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
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
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o kfunc.o kfunc.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o kstring.o kstring.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o bgzf.o bgzf.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o errmod.o errmod.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o faidx.o faidx.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o header.o header.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.19"' > 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' \
'' \
'-Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden' \
'-Wl,--as-needed,-O1,--sort-common -fvisibility=hidden ' \
'-ldeflate -llzma -lbz2 -lz  -lcurl -lcrypto' > config_vars.h
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o hts_expr.o hts_expr.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o hts_os.o hts_os.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o md5.o md5.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o multipart.o multipart.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o probaln.o probaln.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o realn.o realn.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o regidx.o regidx.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o region.o region.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o sam.o sam.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o sam_mods.o sam_mods.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o vcf_sweep.o vcf_sweep.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o tbx.o tbx.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o textutils.o textutils.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o thread_pool.o thread_pool.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o vcf.o vcf.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o vcfutils.o vcfutils.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o cram/cram_io.o cram/cram_io.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o cram/mFILE.o cram/mFILE.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o cram/string_alloc.o cram/string_alloc.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o hfile_libcurl.o hfile_libcurl.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o hfile_gcs.o hfile_gcs.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o hfile_s3.o hfile_s3.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o hfile_s3_write.o hfile_s3_write.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o kfunc.pico kfunc.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o kstring.pico kstring.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o bgzf.pico bgzf.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o errmod.pico errmod.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o faidx.pico faidx.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o header.pico header.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o hfile.pico hfile.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o hts.pico hts.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o hts_expr.pico hts_expr.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o hts_os.pico hts_os.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o md5.pico md5.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o multipart.pico multipart.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o probaln.pico probaln.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o realn.pico realn.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o regidx.pico regidx.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o region.pico region.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o sam.pico sam.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o sam_mods.pico sam_mods.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o tbx.pico tbx.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o textutils.pico textutils.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o thread_pool.pico thread_pool.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o vcf.pico vcf.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o vcfutils.pico vcfutils.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o hfile_gcs.pico hfile_gcs.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o hfile_s3.pico hfile_s3.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -fpic -c -o hfile_s3_write.pico hfile_s3_write.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o annot-tsv.o annot-tsv.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o bgzip.o bgzip.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o htsfile.o htsfile.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o tabix.o tabix.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/hts_endian.o test/hts_endian.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/fieldarith.o test/fieldarith.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/hfile.o test/hfile.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/pileup.o test/pileup.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/pileup_mod.o test/pileup_mod.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/plugins-dlhts.o test/plugins-dlhts.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/sam.o test/sam.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test_bgzf.o test/test_bgzf.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test_expr.o test/test_expr.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test_faidx.o test/test_faidx.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test_kfunc.o test/test_kfunc.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test_kstring.o test/test_kstring.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test_mod.o test/test_mod.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test_realn.o test/test_realn.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test-regidx.o test/test-regidx.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test_str2int.o test/test_str2int.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test_time_funcs.o test/test_time_funcs.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test_view.o test/test_view.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test_index.o test/test_index.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test_introspection.o test/test_introspection.c
gcc -Wall -Os -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.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 -fstack-clash-protection -Wformat -Werror=format-security -fvisibility=hidden  -I.  -c -o hts.o hts.c
gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden  -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -llzma -lbz2 -lz  -lcurl -lcrypto
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/test_time_funcs test/test_time_funcs.o
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 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  hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o
ranlib libhts.a
gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden  -o annot-tsv annot-tsv.o libhts.a -ldeflate -llzma -lbz2 -lz  -lcurl -lcrypto -lpthread
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_faidx test/test_faidx.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
gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -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 sam_mods.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 hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico hfile_s3_write.pico -ldeflate -llzma -lbz2 -lz  -lcurl -lcrypto -lpthread
ln -sf libhts.so libhts.so.3
gcc -Wl,--as-needed,-O1,--sort-common -fvisibility=hidden  -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -ldeflate -llzma -lbz2 -lz  -lcurl -lcrypto -lpthread
>>> htslib: Entering fakeroot...
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.1.19
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib#g;s#@-PACKAGE_VERSION@#1.19#g' htslib.pc.tmp > /home/buildozer/aports/testing/htslib/pkg/htslib/usr/lib/pkgconfig/htslib.pc
ln -sf libhts.so.1.19 /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.1.19 /home/buildozer/aports/testing/htslib/pkg/htslib/usr/lib/libhts.so.3
install -p annot-tsv 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 annot-tsv.1 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=1.19-r0
	pc:bzip2
	pc:liblzma
	pc:zlib
	pkgconfig
>>> htslib-dev*: Package size: 520.0 KB
>>> htslib-dev*: Compressing data...
>>> htslib-dev*: Create checksum...
>>> htslib-dev*: Create htslib-dev-1.19-r0.apk
>>> htslib-doc*: Tracing dependencies...
>>> htslib-doc*: Package size: 60.0 KB
>>> htslib-doc*: Compressing data...
>>> htslib-doc*: Create checksum...
>>> htslib-doc*: Create htslib-doc-1.19-r0.apk
>>> htslib-static*: Tracing dependencies...
>>> htslib-static*: Package size: 812.0 KB
>>> htslib-static*: Compressing data...
>>> htslib-static*: Create checksum...
>>> htslib-static*: Create htslib-static-1.19-r0.apk
>>> htslib-tools*: Tracing dependencies...
	so:libbz2.so.1
	so:libc.musl-armv7.so.1
	so:libcrypto.so.3
	so:libcurl.so.4
	so:libdeflate.so.0
	so:liblzma.so.5
	so:libz.so.1
>>> htslib-tools*: Package size: 1.6 MB
>>> htslib-tools*: Compressing data...
>>> htslib-tools*: Create checksum...
>>> htslib-tools*: Create htslib-tools-1.19-r0.apk
>>> htslib*: Tracing dependencies...
	so:libbz2.so.1
	so:libc.musl-armv7.so.1
	so:libcrypto.so.3
	so:libcurl.so.4
	so:libdeflate.so.0
	so:liblzma.so.5
	so:libz.so.1
>>> htslib*: Package size: 524.0 KB
>>> htslib*: Compressing data...
>>> htslib*: Create checksum...
>>> htslib*: Create htslib-1.19-r0.apk
>>> htslib: Build complete at Tue, 12 Dec 2023 17:44:20 +0000 elapsed time 0h 0m 11s
>>> htslib: Cleaning up srcdir
>>> htslib: Cleaning up pkgdir
>>> htslib: Uninstalling dependencies...
(1/16) Purging .makedepends-htslib (20231212.174410)
(2/16) Purging bzip2-dev (1.0.8-r6)
(3/16) Purging libbz2 (1.0.8-r6)
(4/16) Purging curl-dev (8.5.0-r0)
(5/16) Purging brotli-dev (1.1.0-r1)
(6/16) Purging brotli (1.1.0-r1)
(7/16) Purging c-ares-dev (1.23.0-r0)
(8/16) Purging libidn2-dev (2.3.4-r4)
(9/16) Purging nghttp2-dev (1.58.0-r0)
(10/16) Purging openssl-dev (3.1.4-r2)
(11/16) Purging libdeflate-dev (1.19-r0)
(12/16) Purging libdeflate (1.19-r0)
(13/16) Purging xz-dev (5.4.5-r0)
(14/16) Purging xz (5.4.5-r0)
(15/16) Purging xz-libs (5.4.5-r0)
(16/16) Purging zlib-dev (1.3-r2)
Executing busybox-1.36.1-r16.trigger
OK: 271 MiB in 104 packages
>>> htslib: Updating the testing/armv7 repository index...
>>> htslib: Signing the index...