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libraries/htslib: Update to version 1.23.1#14925

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brobr wants to merge 2 commits intoSlackBuildsOrg:masterfrom
brobr:htslib
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libraries/htslib: Update to version 1.23.1#14925
brobr wants to merge 2 commits intoSlackBuildsOrg:masterfrom
brobr:htslib

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@brobr brobr commented Mar 25, 2026

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reverse dependencies - libraries/htslib

  • academic/bcftools
  • academic/samtools

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github-actions bot commented Mar 25, 2026

✅ sbolint - libraries/htslib ✅

sbolint: htslib checks out OK

Repaired "htslib: ERR: htslib.info:2: missing closing double-quote"
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willysr commented Mar 25, 2026

@sbo-bot: build libraries/htslib

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sbo-bot bot commented Mar 25, 2026

buildpkg i586 libraries/htslib

Creating hintfile directory: /etc/repo/SBo/hintfiles
Checking whether git is clean ... yes.
Indexing SlackBuilds ... done.
git repo: /var/lib/repo/SBo/slackbuilds
branch:   HEAD
date:     Wed Mar 25 12:14:55 GMT 2026
revision: 51d7f3b458afd09fdb61ae6c3d9d4a5a1c79b0c2
title:    Merge 5c178829c32b3ee828343cea2881b91f1e712453 into 77855d4c3396a40dd6bab35bb345cc70b020508d

================================================================================
libraries/htslib                                                        14:26:39
================================================================================

Calculating dependencies ... none.

Building libraries/htslib (update for version 1.23.1) ----------------- 14:26:39
Testing SlackBuild files ... done.
Downloading source files ...
Verifying source files ... done.
Running htslib.SlackBuild ...                                       ETA 14:27:??
env MAKEFLAGS='-j24 -l13' nice -n 5 bash ./htslib.SlackBuild
Built ok:  htslib-1.23.1-i586-1_SBo.txz                                 14:26:59
Testing package htslib-1.23.1-i586-1_SBo.txz ... done.
Test installing htslib-1.23.1-i586-1_SBo.txz ...
htslib-1.23.1-i586-1_SBo: High Troughput Sequencing Library ............ [ 6.7M]
Unmounting chroot ... done.
Backed up: htslib-1.23-i586-1_SBo.txz
✅ libraries/htslib Updated for version 1.23.1 ✅

================================================================================
SUMMARY                                                                 14:27:00
================================================================================

Logfile:     /var/log/repo/SBo/repo_2026-03-25_14:26:38.log
Runtime:     0h 0m 22s
Updated:     1
  libraries/htslib/htslib-1.23.1-i586-1_SBo.txz

Snipped Build Log

Details

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htslib-1.23.1/htscodecs/tests/rans4x16.test
htslib-1.23.1/htscodecs/tests/rANS_static4x16pr_test.c
htslib-1.23.1/htscodecs/tests/rANS_static_fuzz.c
htslib-1.23.1/htscodecs/tests/varint_test.c
htslib-1.23.1/htscodecs/tests/entropy_fuzz.c
htslib-1.23.1/htscodecs/LICENSE.md
htslib-1.23.1/htscodecs/htscodecs/
htslib-1.23.1/htscodecs/htscodecs/utils.c
htslib-1.23.1/htscodecs/htscodecs/rANS_static4x16pr.c
htslib-1.23.1/htscodecs/htscodecs/rANS_word.h
htslib-1.23.1/htscodecs/htscodecs/arith_dynamic.c
htslib-1.23.1/htscodecs/htscodecs/c_range_coder.h
htslib-1.23.1/htscodecs/htscodecs/rANS_byte.h
htslib-1.23.1/htscodecs/htscodecs/arith_dynamic.h
htslib-1.23.1/htscodecs/htscodecs/htscodecs.h
htslib-1.23.1/htscodecs/htscodecs/c_simple_model.h
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htslib-1.23.1/htscodecs/htscodecs/permute.h
htslib-1.23.1/htscodecs/htscodecs/rANS_static.h
htslib-1.23.1/htscodecs/htscodecs/rANS_static4x16.h
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htslib-1.23.1/htscodecs/htscodecs/htscodecs.c
htslib-1.23.1/htscodecs/htscodecs/rANS_static32x16pr_avx512.c
htslib-1.23.1/htscodecs/htscodecs/rANS_static32x16pr_neon.c
htslib-1.23.1/htscodecs/htscodecs/tokenise_name3.h
htslib-1.23.1/htscodecs/htscodecs/varint2.h
htslib-1.23.1/htscodecs/htscodecs/pooled_alloc.h
htslib-1.23.1/htscodecs/htscodecs/htscodecs_endian.h
htslib-1.23.1/htscodecs/htscodecs/rANS_static32x16pr_sse4.c
htslib-1.23.1/htscodecs/htscodecs/rANS_static16_int.h
htslib-1.23.1/htscodecs/htscodecs/tokenise_name3.c
htslib-1.23.1/htscodecs/htscodecs/version.h
htslib-1.23.1/htscodecs/htscodecs/rANS_static32x16pr.c
htslib-1.23.1/htscodecs/htscodecs/rANS_static32x16pr.h
htslib-1.23.1/htscodecs/htscodecs/fqzcomp_qual.h
htslib-1.23.1/htscodecs/MAINTAINERS.md
htslib-1.23.1/config.guess
htslib-1.23.1/regidx.c
htslib-1.23.1/vcf.5
htslib-1.23.1/md5.c
htslib-1.23.1/NEWS
htslib-1.23.1/vcf_sweep.c
htslib-1.23.1/vcfutils.c
htslib-1.23.1/realn.c
htslib-1.23.1/m4/
htslib-1.23.1/m4/hts_hide_dynamic_syms.m4
htslib-1.23.1/m4/hts_prog_cc_warnings.m4
htslib-1.23.1/m4/hts_check_compile_flags_needed.m4
htslib-1.23.1/m4/pkg.m4
htslib-1.23.1/errmod.c
htslib-1.23.1/simd.c
htslib-1.23.1/header.c
htslib-1.23.1/htsfile.c
htslib-1.23.1/faidx.5
checking for 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 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... none
checking C compiler flags needed for avx2... none
checking C compiler flags needed for avx512f... none
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 gcc option to enable large file support... -D_FILE_OFFSET_BITS=64
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... i586-slackware-linux-gnu
checking host system type... i586-slackware-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... -ldl
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... no
checking for libdeflate_deflate_compress in -ldeflate... no
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 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... yes
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... no
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
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o kfunc.o kfunc.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o kstring.o kstring.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o bgzf.o bgzf.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o errmod.o errmod.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o faidx.o faidx.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o header.o header.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.23.1"' > 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 -O2 -march=i586 -mtune=i686 -fvisibility=hidden' \
'-fvisibility=hidden -rdynamic' \
'-llzma -lbz2 -lz -lm -ldl ' > config_vars.h
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o hts_expr.o hts_expr.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o hts_os.o hts_os.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o md5.o md5.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o multipart.o multipart.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o probaln.o probaln.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o realn.o realn.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o regidx.o regidx.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o region.o region.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o sam.o sam.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o sam_mods.o sam_mods.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o simd.o simd.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o vcf_sweep.o vcf_sweep.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o tbx.o tbx.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o textutils.o textutils.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o thread_pool.o thread_pool.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o vcf.o vcf.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o vcfutils.o vcfutils.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o cram/cram_io.o cram/cram_io.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o cram/mFILE.o cram/mFILE.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o cram/string_alloc.o cram/string_alloc.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -DPLUGINPATH=\"/usr/libexec/htslib\" -c -o plugin.o plugin.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o kfunc.pico kfunc.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o kstring.pico kstring.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o bgzf.pico bgzf.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o errmod.pico errmod.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o faidx.pico faidx.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o header.pico header.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o hfile.pico hfile.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o hts.pico hts.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o hts_expr.pico hts_expr.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o hts_os.pico hts_os.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o md5.pico md5.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o multipart.pico multipart.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o probaln.pico probaln.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o realn.pico realn.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o regidx.pico regidx.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o region.pico region.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o sam.pico sam.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o sam_mods.pico sam_mods.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o simd.pico simd.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o tbx.pico tbx.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o textutils.pico textutils.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o thread_pool.pico thread_pool.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o vcf.pico vcf.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o vcfutils.pico vcfutils.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -DPLUGINPATH=\"/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o annot-tsv.o annot-tsv.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o bgzip.o bgzip.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o htsfile.o htsfile.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o tabix.o tabix.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o hfile_gcs.pico hfile_gcs.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -fpic -c -o hfile_s3.pico hfile_s3.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/hts_endian.o test/hts_endian.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/fieldarith.o test/fieldarith.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/hfile.o test/hfile.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/pileup.o test/pileup.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/pileup_mod.o test/pileup_mod.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/plugins-dlhts.o test/plugins-dlhts.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/sam.o test/sam.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_bgzf.o test/test_bgzf.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_expr.o test/test_expr.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_faidx.o test/test_faidx.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_kfunc.o test/test_kfunc.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_khash.o test/test_khash.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_kstring.o test/test_kstring.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_mod.o test/test_mod.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_nibbles.o test/test_nibbles.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_realn.o test/test_realn.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test-regidx.o test/test-regidx.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_str2int.o test/test_str2int.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_time_funcs.o test/test_time_funcs.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_view.o test/test_view.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_index.o test/test_index.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o test/test_introspection.o test/test_introspection.c
gcc -Wall -O2 -march=i586 -mtune=i686 -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 -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/cmsg_wrap.o ref_cache/cmsg_wrap.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/http_parser.o ref_cache/http_parser.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/listener.o ref_cache/listener.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/log_files.o ref_cache/log_files.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/main.o ref_cache/main.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/misc.o ref_cache/misc.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/ping.o ref_cache/ping.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_epoll.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/poll_wrap_poll.o ref_cache/poll_wrap_poll.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/ref_files.o ref_cache/ref_files.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/request_handler.o ref_cache/request_handler.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/sendfile_wrap.o ref_cache/sendfile_wrap.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/server.o ref_cache/server.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/transaction.o ref_cache/transaction.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/upstream.o ref_cache/upstream.c
gcc -Wall -O2 -march=i586 -mtune=i686 -fvisibility=hidden  -I.  -c -o hts.o hts.c
gcc -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm -ldl 
gcc -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm -ldl 
gcc -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o
gcc -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o -lm
gcc -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
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
gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -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 -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_khash test/test_khash.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_nibbles test/test_nibbles.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
ln -sf libhts.so libhts.so.3
gcc -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -shared -Wl,-E -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm -ldl  -lcurl -lpthread
gcc -shared -Wl,-E -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -shared -Wl,-E -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -ldl  -lcrypto -lcurl -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
mkdir -p -m 755 /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/bin /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/include /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/include/htslib /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/lib /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/man/man1 /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/man/man5 /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/man/man7 /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/lib/pkgconfig
if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/libexec/htslib; fi
install -p -m 644 libhts.so /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/lib/libhts.so.1.23.1
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib#g;s#@-PACKAGE_VERSION@#1.23.1#g' htslib.pc.tmp > /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/lib/pkgconfig/htslib.pc
ln -sf libhts.so.1.23.1 /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/lib/libhts.so
chmod 644 /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/lib/pkgconfig/htslib.pc
ln -sf libhts.so.1.23.1 /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/lib/libhts.so.3
install -p annot-tsv bgzip htsfile tabix ref_cache/ref-cache /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/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 /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/libexec/htslib; fi
install -p -m 644 htslib/*.h /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/include/htslib
install -p -m 644 libhts.a /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/lib/libhts.a
install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/man/man1
if test "xref_cache/ref-cache" != "x" ; then \
    install -p -m 644 ref_cache/ref-cache.1 /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/man/man1 ; \
fi
install -p -m 644 faidx.5 sam.5 vcf.5 /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/man/man5
install -p -m 644 htslib-s3-plugin.7 /tmp/SBo/repo.FDars3/build_htslib/package-htslib/usr/man/man7

Slackware package maker, version 3.14159265.

Searching for symbolic links:
usr/lib/libhts.so	libhts.so.1.23.1
usr/lib/libhts.so.3	libhts.so.1.23.1

Making symbolic link creation script:
( cd usr/lib ; rm -rf libhts.so )
( cd usr/lib ; ln -sf libhts.so.1.23.1 libhts.so )
( cd usr/lib ; rm -rf libhts.so.3 )
( cd usr/lib ; ln -sf libhts.so.1.23.1 libhts.so.3 )

It is recommended that you make these lines your new installation script.

Would you like to make this stuff the install script for this package
and remove the symbolic links ([y]es, [n]o)? y


Removing symbolic links:
removed './usr/lib/libhts.so'
removed './usr/lib/libhts.so.3'

Creating your new ./install/doinst.sh...

This next step is optional - you can set the directories in your package
to some sane permissions. If any of the directories in your package have
special permissions, then DO NOT reset them here!

Would you like to reset all directory permissions to 755 (drwxr-xr-x) and
directory ownerships to root.root ([y]es, [n]o)? n


Creating Slackware package:  /tmp/SBo/repo.FDars3/output_htslib/htslib-1.23.1-i586-1_SBo.txz

./
install/
install/doinst.sh
install/slack-desc
usr/
usr/bin/
usr/bin/annot-tsv
usr/bin/bgzip
usr/bin/htsfile
usr/bin/ref-cache
usr/bin/tabix
usr/doc/
usr/doc/htslib-1.23.1/
usr/doc/htslib-1.23.1/LICENSE
usr/doc/htslib-1.23.1/NEWS
usr/doc/htslib-1.23.1/README
usr/doc/htslib-1.23.1/htslib.SlackBuild
usr/include/
usr/include/htslib/
usr/include/htslib/bgzf.h
usr/include/htslib/cram.h
usr/include/htslib/faidx.h
usr/include/htslib/hfile.h
usr/include/htslib/hts.h
usr/include/htslib/hts_defs.h
usr/include/htslib/hts_endian.h
usr/include/htslib/hts_expr.h
usr/include/htslib/hts_log.h
usr/include/htslib/hts_os.h
usr/include/htslib/kbitset.h
usr/include/htslib/kfunc.h
usr/include/htslib/khash.h
usr/include/htslib/khash_str2int.h
usr/include/htslib/klist.h
usr/include/htslib/knetfile.h
usr/include/htslib/kroundup.h
usr/include/htslib/kseq.h
usr/include/htslib/ksort.h
usr/include/htslib/kstring.h
usr/include/htslib/regidx.h
usr/include/htslib/sam.h
usr/include/htslib/synced_bcf_reader.h
usr/include/htslib/tbx.h
usr/include/htslib/thread_pool.h
usr/include/htslib/vcf.h
usr/include/htslib/vcf_sweep.h
usr/include/htslib/vcfutils.h
usr/lib/
usr/lib/libhts.a
usr/lib/libhts.so.1.23.1
usr/lib/pkgconfig/
usr/lib/pkgconfig/htslib.pc
usr/libexec/
usr/libexec/htslib/
usr/libexec/htslib/hfile_gcs.so
usr/libexec/htslib/hfile_libcurl.so
usr/libexec/htslib/hfile_s3.so
usr/man/
usr/man/man1/
usr/man/man1/annot-tsv.1.gz
usr/man/man1/bgzip.1.gz
usr/man/man1/htsfile.1.gz
usr/man/man1/ref-cache.1.gz
usr/man/man1/tabix.1.gz
usr/man/man5/
usr/man/man5/faidx.5.gz
usr/man/man5/sam.5.gz
usr/man/man5/vcf.5.gz
usr/man/man7/
usr/man/man7/htslib-s3-plugin.7.gz

Slackware package /tmp/SBo/repo.FDars3/output_htslib/htslib-1.23.1-i586-1_SBo.txz created.

Built ok:  htslib-1.23.1-i586-1_SBo.txz                                 14:26:59
Testing package htslib-1.23.1-i586-1_SBo.txz ... 
Test installing htslib-1.23.1-i586-1_SBo.txz ...
htslib-1.23.1-i586-1_SBo: High Troughput Sequencing Library ............ [ 6.7M]
Unmounting chroot ... 
Backed up: htslib-1.23-i586-1_SBo.txz
:-) libraries/htslib Updated for version 1.23.1 (-:

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sbo-bot bot commented Mar 25, 2026

sbopkglint i586 libraries/htslib

Using tests from /usr/share/sbo-maintainer-tools/sbopkglint.d
Exploding /var/lib/repo/SBo/packages/15.0/i586/libraries/htslib/htslib-1.23.1-i586-1_SBo.txz to /tmp/SBo/sbopkglint.LNFfSD ...OK
Running pre-doinst test...OK
Installing /var/lib/repo/SBo/packages/15.0/i586/libraries/htslib/htslib-1.23.1-i586-1_SBo.txz to /tmp/SBo/sbopkglint.LNFfSD ...OK
Running test: 05-basic-sanity...OK
Running test: 10-docs...OK
Running test: 15-noarch...OK
Running test: 20-arch...
--- ELF binaries/libraries should be executable:
-rw-r--r-- 1 root root 1134012 Mar 25 14:26 usr/lib/libhts.so.1.23.1
FAILED
Running test: 25-lafiles...OK
Running test: 30-manpages...OK
Running test: 35-desktop...OK
Running test: 40-newconfig...OK
Running test: 45-doinst...OK
Running test: 50-icons...OK
Running test: 60-usr_info...OK
Running test: 65-python...OK
Running test: 70-tmp_path...OK
Running test: 75-static_libs...
___ note: usr/lib has both libhts.so and libhts.a; unless it's needed by a dependee, consider removing libhts.a
OK
Running test: 85-perl...OK
Running test: 90-terminfo...OK
⛔️ !!! htslib-1.23.1-i586-1_SBo.txz: 1 failures ⛔️

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sbo-bot bot commented Mar 25, 2026

buildpkg x86_64 libraries/htslib

Creating hintfile directory: /etc/repo/SBo/hintfiles
Checking whether git is clean ... yes.
Indexing SlackBuilds ... done.
git repo: /var/lib/repo/SBo/slackbuilds
branch:   HEAD
date:     Wed Mar 25 12:14:55 GMT 2026
revision: 51d7f3b458afd09fdb61ae6c3d9d4a5a1c79b0c2
title:    Merge 5c178829c32b3ee828343cea2881b91f1e712453 into 77855d4c3396a40dd6bab35bb345cc70b020508d

================================================================================
libraries/htslib                                                        14:28:01
================================================================================

Calculating dependencies ... none.

Building libraries/htslib (update for version 1.23.1) ----------------- 14:28:02
Testing SlackBuild files ... done.
Downloading source files ...
Verifying source files ... done.
Running htslib.SlackBuild ...                                       ETA 14:28:??
env MAKEFLAGS='-j24 -l13' nice -n 5 bash ./htslib.SlackBuild
Built ok:  htslib-1.23.1-x86_64-1_SBo.txz                               14:28:21
Testing package htslib-1.23.1-x86_64-1_SBo.txz ... done.
Test installing htslib-1.23.1-x86_64-1_SBo.txz ...
htslib-1.23.1-x86_64-1_SBo: High Troughput Sequencing Library .......... [ 7.0M]
Unmounting chroot ... done.
Backed up: htslib-1.23-x86_64-1_SBo.txz
✅ libraries/htslib Updated for version 1.23.1 ✅

================================================================================
SUMMARY                                                                 14:28:22
================================================================================

Logfile:     /var/log/repo/SBo/repo_2026-03-25_14:28:01.log
Runtime:     0h 0m 22s
Updated:     1
  libraries/htslib/htslib-1.23.1-x86_64-1_SBo.txz

Snipped Build Log

Details
rnal.h
htslib-1.23.1/hts.c
htslib-1.23.1/tabix.1
htslib-1.23.1/config.mk.in
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htslib-1.23.1/htscodecs/
htslib-1.23.1/htscodecs/BENCHMARKS.md
htslib-1.23.1/htscodecs/NEWS.md
htslib-1.23.1/htscodecs/tests/
htslib-1.23.1/htscodecs/tests/benchmark.sh
htslib-1.23.1/htscodecs/tests/entropy.c
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htslib-1.23.1/htscodecs/tests/names/tok3/08.names.19
htslib-1.23.1/htscodecs/tests/names/tok3/nv2.names.3
htslib-1.23.1/htscodecs/tests/names/tok3/08.names.11
htslib-1.23.1/htscodecs/tests/names/tok3/rr.names.13
htslib-1.23.1/htscodecs/tests/names/tok3/05.names.13
htslib-1.23.1/htscodecs/tests/names/tok3/nv.names.11
htslib-1.23.1/htscodecs/tests/names/tok3/05.names.11
htslib-1.23.1/htscodecs/tests/names/tok3/nv2.names.11
htslib-1.23.1/htscodecs/tests/names/tok3/03.names.19
htslib-1.23.1/htscodecs/tests/names/tok3/02.names.11
htslib-1.23.1/htscodecs/tests/names/tok3/05.names.15
htslib-1.23.1/htscodecs/tests/names/tok3/01.names.11
htslib-1.23.1/htscodecs/tests/names/tok3/rr.names.9
htslib-1.23.1/htscodecs/tests/names/tok3/20.names.15
htslib-1.23.1/htscodecs/tests/names/tok3/02.names.15
htslib-1.23.1/htscodecs/tests/names/tok3/09.names.5
htslib-1.23.1/htscodecs/tests/names/tok3/09.names.17
htslib-1.23.1/htscodecs/tests/names/tok3/nv2.names.9
htslib-1.23.1/htscodecs/tests/names/tok3/20.names.19
htslib-1.23.1/htscodecs/tests/names/tok3/20.names.9
htslib-1.23.1/htscodecs/tests/names/tok3/01.names.7
htslib-1.23.1/htscodecs/tests/names/tok3/rr.names.7
htslib-1.23.1/htscodecs/tests/names/tok3/02.names.17
htslib-1.23.1/htscodecs/tests/names/tok3/nv.names.9
htslib-1.23.1/htscodecs/tests/names/tok3/20.names.13
htslib-1.23.1/htscodecs/tests/names/10.names
htslib-1.23.1/htscodecs/tests/names/08.names
htslib-1.23.1/htscodecs/tests/names/03.names
htslib-1.23.1/htscodecs/tests/names/rr.names
htslib-1.23.1/htscodecs/tests/rans4x16.test
htslib-1.23.1/htscodecs/tests/rANS_static4x16pr_test.c
htslib-1.23.1/htscodecs/tests/rANS_static_fuzz.c
htslib-1.23.1/htscodecs/tests/varint_test.c
htslib-1.23.1/htscodecs/tests/entropy_fuzz.c
htslib-1.23.1/htscodecs/LICENSE.md
htslib-1.23.1/htscodecs/htscodecs/
htslib-1.23.1/htscodecs/htscodecs/utils.c
htslib-1.23.1/htscodecs/htscodecs/rANS_static4x16pr.c
htslib-1.23.1/htscodecs/htscodecs/rANS_word.h
htslib-1.23.1/htscodecs/htscodecs/arith_dynamic.c
htslib-1.23.1/htscodecs/htscodecs/c_range_coder.h
htslib-1.23.1/htscodecs/htscodecs/rANS_byte.h
htslib-1.23.1/htscodecs/htscodecs/arith_dynamic.h
htslib-1.23.1/htscodecs/htscodecs/htscodecs.h
htslib-1.23.1/htscodecs/htscodecs/c_simple_model.h
htslib-1.23.1/htscodecs/htscodecs/rle.c
htslib-1.23.1/htscodecs/htscodecs/rle.h
htslib-1.23.1/htscodecs/htscodecs/fqzcomp_qual.c
htslib-1.23.1/htscodecs/htscodecs/varint.h
htslib-1.23.1/htscodecs/htscodecs/pack.h
htslib-1.23.1/htscodecs/htscodecs/rANS_static32x16pr_avx2.c
htslib-1.23.1/htscodecs/htscodecs/rANS_static.c
htslib-1.23.1/htscodecs/htscodecs/pack.c
htslib-1.23.1/htscodecs/htscodecs/permute.h
htslib-1.23.1/htscodecs/htscodecs/rANS_static.h
htslib-1.23.1/htscodecs/htscodecs/rANS_static4x16.h
htslib-1.23.1/htscodecs/htscodecs/utils.h
htslib-1.23.1/htscodecs/htscodecs/htscodecs.c
htslib-1.23.1/htscodecs/htscodecs/rANS_static32x16pr_avx512.c
htslib-1.23.1/htscodecs/htscodecs/rANS_static32x16pr_neon.c
htslib-1.23.1/htscodecs/htscodecs/tokenise_name3.h
htslib-1.23.1/htscodecs/htscodecs/varint2.h
htslib-1.23.1/htscodecs/htscodecs/pooled_alloc.h
htslib-1.23.1/htscodecs/htscodecs/htscodecs_endian.h
htslib-1.23.1/htscodecs/htscodecs/rANS_static32x16pr_sse4.c
htslib-1.23.1/htscodecs/htscodecs/rANS_static16_int.h
htslib-1.23.1/htscodecs/htscodecs/tokenise_name3.c
htslib-1.23.1/htscodecs/htscodecs/version.h
htslib-1.23.1/htscodecs/htscodecs/rANS_static32x16pr.c
htslib-1.23.1/htscodecs/htscodecs/rANS_static32x16pr.h
htslib-1.23.1/htscodecs/htscodecs/fqzcomp_qual.h
htslib-1.23.1/htscodecs/MAINTAINERS.md
htslib-1.23.1/config.guess
htslib-1.23.1/regidx.c
htslib-1.23.1/vcf.5
htslib-1.23.1/md5.c
htslib-1.23.1/NEWS
htslib-1.23.1/vcf_sweep.c
htslib-1.23.1/vcfutils.c
htslib-1.23.1/realn.c
htslib-1.23.1/m4/
htslib-1.23.1/m4/hts_hide_dynamic_syms.m4
htslib-1.23.1/m4/hts_prog_cc_warnings.m4
htslib-1.23.1/m4/hts_check_compile_flags_needed.m4
htslib-1.23.1/m4/pkg.m4
htslib-1.23.1/errmod.c
htslib-1.23.1/simd.c
htslib-1.23.1/header.c
htslib-1.23.1/htsfile.c
htslib-1.23.1/faidx.5
checking for 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 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... /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 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-slackware-linux-gnu
checking host system type... x86_64-slackware-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... -ldl
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... no
checking for libdeflate_deflate_compress in -ldeflate... no
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 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... yes
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
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o kfunc.o kfunc.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o kstring.o kstring.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o bgzf.o bgzf.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o errmod.o errmod.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o faidx.o faidx.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o header.o header.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.23.1"' > 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 -O2 -fPIC -fvisibility=hidden' \
'-fvisibility=hidden -rdynamic' \
'-llzma -lbz2 -lz -lm -ldl ' > config_vars.h
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o hts_expr.o hts_expr.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o hts_os.o hts_os.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o md5.o md5.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o multipart.o multipart.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o probaln.o probaln.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o realn.o realn.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o regidx.o regidx.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o region.o region.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o sam.o sam.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o sam_mods.o sam_mods.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o simd.o simd.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o vcf_sweep.o vcf_sweep.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o tbx.o tbx.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o textutils.o textutils.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o thread_pool.o thread_pool.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o vcf.o vcf.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o vcfutils.o vcfutils.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o cram/cram_io.o cram/cram_io.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o cram/mFILE.o cram/mFILE.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o cram/string_alloc.o cram/string_alloc.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -mavx2 -mpopcnt -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -mavx512f -mpopcnt -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -DPLUGINPATH=\"/usr/libexec/htslib\" -c -o plugin.o plugin.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o kfunc.pico kfunc.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o kstring.pico kstring.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o bgzf.pico bgzf.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o errmod.pico errmod.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o faidx.pico faidx.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o header.pico header.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o hfile.pico hfile.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o hts.pico hts.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o hts_expr.pico hts_expr.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o hts_os.pico hts_os.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o md5.pico md5.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o multipart.pico multipart.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o probaln.pico probaln.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o realn.pico realn.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o regidx.pico regidx.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o region.pico region.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o sam.pico sam.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o sam_mods.pico sam_mods.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o simd.pico simd.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o tbx.pico tbx.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o textutils.pico textutils.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o thread_pool.pico thread_pool.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o vcf.pico vcf.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o vcfutils.pico vcfutils.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -mavx2 -mpopcnt -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -mavx512f -mpopcnt -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -DPLUGINPATH=\"/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o annot-tsv.o annot-tsv.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o bgzip.o bgzip.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o htsfile.o htsfile.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o tabix.o tabix.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o hfile_gcs.pico hfile_gcs.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -fpic -c -o hfile_s3.pico hfile_s3.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/hts_endian.o test/hts_endian.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/fieldarith.o test/fieldarith.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/hfile.o test/hfile.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/pileup.o test/pileup.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/pileup_mod.o test/pileup_mod.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/plugins-dlhts.o test/plugins-dlhts.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/sam.o test/sam.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_bgzf.o test/test_bgzf.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_expr.o test/test_expr.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_faidx.o test/test_faidx.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_kfunc.o test/test_kfunc.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_khash.o test/test_khash.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_kstring.o test/test_kstring.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_mod.o test/test_mod.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_nibbles.o test/test_nibbles.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_realn.o test/test_realn.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test-regidx.o test/test-regidx.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_str2int.o test/test_str2int.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_time_funcs.o test/test_time_funcs.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_view.o test/test_view.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_index.o test/test_index.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o test/test_introspection.o test/test_introspection.c
gcc -Wall -O2 -fPIC -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 -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/cmsg_wrap.o ref_cache/cmsg_wrap.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/http_parser.o ref_cache/http_parser.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/listener.o ref_cache/listener.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/log_files.o ref_cache/log_files.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/main.o ref_cache/main.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/misc.o ref_cache/misc.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/ping.o ref_cache/ping.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_epoll.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/poll_wrap_poll.o ref_cache/poll_wrap_poll.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/ref_files.o ref_cache/ref_files.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/request_handler.o ref_cache/request_handler.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/sendfile_wrap.o ref_cache/sendfile_wrap.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/server.o ref_cache/server.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/transaction.o ref_cache/transaction.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/upstream.o ref_cache/upstream.c
gcc -Wall -O2 -fPIC -fvisibility=hidden  -I.  -c -o hts.o hts.c
gcc -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm -ldl 
gcc -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm -ldl 
gcc -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o
gcc -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o -lm
gcc -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
gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -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 -llzma -lbz2 -lz -lm -ldl  -lpthread
ln -sf libhts.so libhts.so.3
gcc -shared -Wl,-E -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm -ldl  -lcurl -lpthread
gcc -shared -Wl,-E -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -shared -Wl,-E -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -ldl  -lcrypto -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
gcc -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_khash test/test_khash.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_nibbles test/test_nibbles.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
gcc -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -llzma -lbz2 -lz -lm -ldl  -lpthread
mkdir -p -m 755 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/bin /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/include /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/include/htslib /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/lib64 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/man/man1 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/man/man5 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/man/man7 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/lib64/pkgconfig
if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/libexec/htslib; fi
install -p -m 644 libhts.so /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/lib64/libhts.so.1.23.1
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.23.1#g' htslib.pc.tmp > /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/lib64/pkgconfig/htslib.pc
chmod 644 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/lib64/pkgconfig/htslib.pc
ln -sf libhts.so.1.23.1 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/lib64/libhts.so
ln -sf libhts.so.1.23.1 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/lib64/libhts.so.3
install -p annot-tsv bgzip htsfile tabix ref_cache/ref-cache /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/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 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/libexec/htslib; fi
install -p -m 644 htslib/*.h /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/include/htslib
install -p -m 644 libhts.a /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/lib64/libhts.a
install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/man/man1
if test "xref_cache/ref-cache" != "x" ; then \
    install -p -m 644 ref_cache/ref-cache.1 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/man/man1 ; \
fi
install -p -m 644 faidx.5 sam.5 vcf.5 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/man/man5
install -p -m 644 htslib-s3-plugin.7 /tmp/SBo/repo.BD0qAv/build_htslib/package-htslib/usr/man/man7

Slackware package maker, version 3.14159265.

Searching for symbolic links:
usr/lib64/libhts.so	libhts.so.1.23.1
usr/lib64/libhts.so.3	libhts.so.1.23.1

Making symbolic link creation script:
( cd usr/lib64 ; rm -rf libhts.so )
( cd usr/lib64 ; ln -sf libhts.so.1.23.1 libhts.so )
( cd usr/lib64 ; rm -rf libhts.so.3 )
( cd usr/lib64 ; ln -sf libhts.so.1.23.1 libhts.so.3 )

It is recommended that you make these lines your new installation script.

Would you like to make this stuff the install script for this package
and remove the symbolic links ([y]es, [n]o)? y


Removing symbolic links:
removed './usr/lib64/libhts.so'
removed './usr/lib64/libhts.so.3'

Creating your new ./install/doinst.sh...

This next step is optional - you can set the directories in your package
to some sane permissions. If any of the directories in your package have
special permissions, then DO NOT reset them here!

Would you like to reset all directory permissions to 755 (drwxr-xr-x) and
directory ownerships to root.root ([y]es, [n]o)? n


Creating Slackware package:  /tmp/SBo/repo.BD0qAv/output_htslib/htslib-1.23.1-x86_64-1_SBo.txz

./
install/
install/doinst.sh
install/slack-desc
usr/
usr/bin/
usr/bin/annot-tsv
usr/bin/bgzip
usr/bin/htsfile
usr/bin/ref-cache
usr/bin/tabix
usr/doc/
usr/doc/htslib-1.23.1/
usr/doc/htslib-1.23.1/LICENSE
usr/doc/htslib-1.23.1/NEWS
usr/doc/htslib-1.23.1/README
usr/doc/htslib-1.23.1/htslib.SlackBuild
usr/include/
usr/include/htslib/
usr/include/htslib/bgzf.h
usr/include/htslib/cram.h
usr/include/htslib/faidx.h
usr/include/htslib/hfile.h
usr/include/htslib/hts.h
usr/include/htslib/hts_defs.h
usr/include/htslib/hts_endian.h
usr/include/htslib/hts_expr.h
usr/include/htslib/hts_log.h
usr/include/htslib/hts_os.h
usr/include/htslib/kbitset.h
usr/include/htslib/kfunc.h
usr/include/htslib/khash.h
usr/include/htslib/khash_str2int.h
usr/include/htslib/klist.h
usr/include/htslib/knetfile.h
usr/include/htslib/kroundup.h
usr/include/htslib/kseq.h
usr/include/htslib/ksort.h
usr/include/htslib/kstring.h
usr/include/htslib/regidx.h
usr/include/htslib/sam.h
usr/include/htslib/synced_bcf_reader.h
usr/include/htslib/tbx.h
usr/include/htslib/thread_pool.h
usr/include/htslib/vcf.h
usr/include/htslib/vcf_sweep.h
usr/include/htslib/vcfutils.h
usr/lib64/
usr/lib64/libhts.a
usr/lib64/libhts.so.1.23.1
usr/lib64/pkgconfig/
usr/lib64/pkgconfig/htslib.pc
usr/libexec/
usr/libexec/htslib/
usr/libexec/htslib/hfile_gcs.so
usr/libexec/htslib/hfile_libcurl.so
usr/libexec/htslib/hfile_s3.so
usr/man/
usr/man/man1/
usr/man/man1/annot-tsv.1.gz
usr/man/man1/bgzip.1.gz
usr/man/man1/htsfile.1.gz
usr/man/man1/ref-cache.1.gz
usr/man/man1/tabix.1.gz
usr/man/man5/
usr/man/man5/faidx.5.gz
usr/man/man5/sam.5.gz
usr/man/man5/vcf.5.gz
usr/man/man7/
usr/man/man7/htslib-s3-plugin.7.gz

Slackware package /tmp/SBo/repo.BD0qAv/output_htslib/htslib-1.23.1-x86_64-1_SBo.txz created.

Built ok:  htslib-1.23.1-x86_64-1_SBo.txz                               14:28:21
Testing package htslib-1.23.1-x86_64-1_SBo.txz ... 
Test installing htslib-1.23.1-x86_64-1_SBo.txz ...
htslib-1.23.1-x86_64-1_SBo: High Troughput Sequencing Library .......... [ 7.0M]
Unmounting chroot ... 
Backed up: htslib-1.23-x86_64-1_SBo.txz
:-) libraries/htslib Updated for version 1.23.1 (-:

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sbo-bot bot commented Mar 25, 2026

sbopkglint x86_64 libraries/htslib

Using tests from /usr/share/sbo-maintainer-tools/sbopkglint.d
Exploding /var/lib/repo/SBo/packages/15.0/x86_64/libraries/htslib/htslib-1.23.1-x86_64-1_SBo.txz to /tmp/SBo/sbopkglint.DRnuFk ...OK
Running pre-doinst test...OK
Installing /var/lib/repo/SBo/packages/15.0/x86_64/libraries/htslib/htslib-1.23.1-x86_64-1_SBo.txz to /tmp/SBo/sbopkglint.DRnuFk ...OK
Running test: 05-basic-sanity...OK
Running test: 10-docs...OK
Running test: 15-noarch...OK
Running test: 20-arch...
--- ELF binaries/libraries should be executable:
-rw-r--r-- 1 root root 1087352 Mar 25 14:28 usr/lib64/libhts.so.1.23.1
FAILED
Running test: 25-lafiles...OK
Running test: 30-manpages...OK
Running test: 35-desktop...OK
Running test: 40-newconfig...OK
Running test: 45-doinst...OK
Running test: 50-icons...OK
Running test: 60-usr_info...OK
Running test: 65-python...OK
Running test: 70-tmp_path...OK
Running test: 75-static_libs...___ note: usr/lib64 has both libhts.so and libhts.a; unless it's needed by a dependee, consider removing libhts.a

OK
Running test: 85-perl...OK
Running test: 90-terminfo...OK
⛔️ !!! htslib-1.23.1-x86_64-1_SBo.txz: 1 failures ⛔️

@willysr
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willysr commented Mar 25, 2026

merged

@willysr willysr closed this Mar 25, 2026
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2 participants