=>> Building biology/htslib build started at Tue Jul 7 06:38:19 JST 2026 port directory: /usr/ports/biology/htslib package name: htslib-1.23.1 building for: FreeBSD s15amd64-setuptools2-job-08 15.1-STABLE FreeBSD 15.1-STABLE 1501501 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1212 Apr 13 23:05 /usr/ports/biology/htslib/Makefile Ports top last git commit: 18628b9022c9c1c0e7cb5e71c2aa1e1e563ca34a Ports top unclean checkout: yes Port dir last git commit: 89c7d793da2638cfdc15252825a5548c3eb2f147 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8 Host OSVERSION: 1501501 Jail OSVERSION: 1501501 Job Id: 08 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1501501 UNAME_v=FreeBSD 15.1-STABLE 1501501 UNAME_r=15.1-STABLE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.8 MASTERMNT=/usr/local/poudriere/data/.m/s15amd64-setuptools2/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/usr/local/poudriere/data/.m/s15amd64-setuptools2/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=s15amd64-setuptools2 SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/s15amd64-setuptools2/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for htslib-1.23.1: CURL=on: Use libcurl for network file access (HTTPS and S3 support). PLUGINS=on: Build and/or install plugins ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --enable-libcurl --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/htslib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/htslib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/htslib/work/.cache HOME=/wrkdirs/usr/ports/biology/htslib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/htslib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/htslib/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.73 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 OPENSSLBASE=/usr/local OPENSSLDIR=/usr/local/openssl OPENSSLINC=/usr/local/include OPENSSLLIB=/usr/local/lib OPENSSLRPATH=/usr/local/lib XDG_DATA_HOME=/wrkdirs/usr/ports/biology/htslib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/htslib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/htslib/work/.cache HOME=/wrkdirs/usr/ports/biology/htslib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/htslib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/htslib/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.73 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -Wl,-rpath,/usr/local/lib -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTVERSION="1.23.1" OSREL=15.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.2 PERL_VER=5.42 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.42 DOCSDIR="share/doc/htslib" EXAMPLESDIR="share/examples/htslib" DATADIR="share/htslib" WWWDIR="www/htslib" ETCDIR="etc/htslib" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/htslib DOCSDIR=/usr/local/share/doc/htslib EXAMPLESDIR=/usr/local/share/examples/htslib WWWDIR=/usr/local/www/htslib ETCDIR=/usr/local/etc/htslib --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles OVERLAYS+=/overlays/overlay_setuptools FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### LICENSES_ACCEPTED= EULA ISC MPEG2ENC DEFAULT_VERSIONS+= magick=7 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= samba=4.23 DEFAULT_VERSIONS+= ssl=openssl japanese_fcitx5-mozc_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_UNSET= JAWIKI x11_wm_hikari_SET= INPUTMETHOD GAMMA LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif #### #### devel_gamin_set= LIBINOTIFY #### Misc Poudriere #### .include "/etc/make.conf.ports_env" DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (kbytes, -y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License BSD3CLAUSE MIT accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> htslib-1.23.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.7.5.pkg [s15amd64-setuptools2-job-08] Installing pkg-2.7.5... [s15amd64-setuptools2-job-08] Extracting pkg-2.7.5: .......... done ===> htslib-1.23.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of htslib-1.23.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE MIT accepted by the user => htslib-1.23.1.tar.bz2 doesn't seem to exist in /portdistfiles. => Attempting to fetch https://github.com/samtools/htslib/releases/download/1.23.1/htslib-1.23.1.tar.bz2 htslib-1.23.1.tar.bz2 4870 kB 60 MBps 01s ===> Fetching all distfiles required by htslib-1.23.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE MIT accepted by the user ===> Fetching all distfiles required by htslib-1.23.1 for building => SHA256 Checksum OK for htslib-1.23.1.tar.bz2. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License BSD3CLAUSE MIT accepted by the user ===> Fetching all distfiles required by htslib-1.23.1 for building ===> Extracting for htslib-1.23.1 => SHA256 Checksum OK for htslib-1.23.1.tar.bz2. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for htslib-1.23.1 ===> Applying FreeBSD patches for htslib-1.23.1 from /usr/ports/biology/htslib/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> htslib-1.23.1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [s15amd64-setuptools2-job-08] Installing gmake-4.4.1... [s15amd64-setuptools2-job-08] `-- Installing gettext-runtime-1.0_1... [s15amd64-setuptools2-job-08] | `-- Installing indexinfo-0.3.1_1... [s15amd64-setuptools2-job-08] | `-- Extracting indexinfo-0.3.1_1: .... done [s15amd64-setuptools2-job-08] `-- Extracting gettext-runtime-1.0_1: .......... done [s15amd64-setuptools2-job-08] Extracting gmake-4.4.1: .......... done ===> htslib-1.23.1 depends on package: gmake>=4.4.1 - found ===> Returning to build of htslib-1.23.1 ===> htslib-1.23.1 depends on file: /usr/local/lib/libcrypto.so.12 - not found ===> Installing existing package /packages/All/openssl-3.0.21,1.pkg [s15amd64-setuptools2-job-08] Installing openssl-3.0.21,1... [s15amd64-setuptools2-job-08] Extracting openssl-3.0.21,1: .......... done ===== Message from openssl-3.0.21,1: -- This port (security/openssl) will update from 3.0 to 3.5 per 2026-07-01 (2026Q3) in anticipation of the End-of-Life of OpenSSL 3.0. A new port (security/openssl30) will be created for the remainder of the lifespan of OpenSSL 3.0 and FreeBSD 14. See: https://openssl-library.org/roadmap/index.html ===> htslib-1.23.1 depends on file: /usr/local/lib/libcrypto.so.12 - found ===> Returning to build of htslib-1.23.1 ===> htslib-1.23.1 depends on package: autoconf>=2.73 - not found ===> Installing existing package /packages/All/autoconf-2.73.pkg [s15amd64-setuptools2-job-08] Installing autoconf-2.73... [s15amd64-setuptools2-job-08] `-- Installing autoconf-switch-20220527... [s15amd64-setuptools2-job-08] `-- Extracting autoconf-switch-20220527: .......... done [s15amd64-setuptools2-job-08] `-- Installing m4-1.4.21,1... [s15amd64-setuptools2-job-08] `-- Extracting m4-1.4.21,1: .......... done [s15amd64-setuptools2-job-08] `-- Installing perl5-5.42.2... [s15amd64-setuptools2-job-08] `-- Extracting perl5-5.42.2: .......... done [s15amd64-setuptools2-job-08] Extracting autoconf-2.73: .......... done ===> htslib-1.23.1 depends on package: autoconf>=2.73 - found ===> Returning to build of htslib-1.23.1 ===> htslib-1.23.1 depends on package: automake>=1.18.1 - not found ===> Installing existing package /packages/All/automake-1.18.1.pkg [s15amd64-setuptools2-job-08] Installing automake-1.18.1... [s15amd64-setuptools2-job-08] Extracting automake-1.18.1: .......... done ===> htslib-1.23.1 depends on package: automake>=1.18.1 - found ===> Returning to build of htslib-1.23.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> htslib-1.23.1 depends on shared library: libdeflate.so - not found ===> Installing existing package /packages/All/libdeflate-1.25.pkg [s15amd64-setuptools2-job-08] Installing libdeflate-1.25... [s15amd64-setuptools2-job-08] Extracting libdeflate-1.25: .......... done ===> htslib-1.23.1 depends on shared library: libdeflate.so - found (/usr/local/lib/libdeflate.so) ===> Returning to build of htslib-1.23.1 ===> htslib-1.23.1 depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-8.21.0.pkg [s15amd64-setuptools2-job-08] Installing curl-8.21.0... [s15amd64-setuptools2-job-08] `-- Installing brotli-1.2.0,1... [s15amd64-setuptools2-job-08] `-- Extracting brotli-1.2.0,1: .......... done [s15amd64-setuptools2-job-08] `-- Installing libidn2-2.3.8... [s15amd64-setuptools2-job-08] | `-- Installing libunistring-1.4.2... [s15amd64-setuptools2-job-08] | `-- Extracting libunistring-1.4.2: .......... done [s15amd64-setuptools2-job-08] `-- Extracting libidn2-2.3.8: .......... done [s15amd64-setuptools2-job-08] `-- Installing libnghttp2-1.69.0... [s15amd64-setuptools2-job-08] `-- Extracting libnghttp2-1.69.0: .......... done [s15amd64-setuptools2-job-08] `-- Installing libpsl-0.22.0... [s15amd64-setuptools2-job-08] `-- Extracting libpsl-0.22.0: .......... done [s15amd64-setuptools2-job-08] `-- Installing libssh2-1.11.1_1,3... [s15amd64-setuptools2-job-08] `-- Extracting libssh2-1.11.1_1,3: .......... done [s15amd64-setuptools2-job-08] `-- Installing zstd-1.5.7_2... [s15amd64-setuptools2-job-08] | `-- Installing liblz4-1.10.0_2,1... [s15amd64-setuptools2-job-08] | `-- Extracting liblz4-1.10.0_2,1: .......... done [s15amd64-setuptools2-job-08] `-- Extracting zstd-1.5.7_2: .......... done [s15amd64-setuptools2-job-08] Extracting curl-8.21.0: .......... done ===> htslib-1.23.1 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of htslib-1.23.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for htslib-1.23.1 configure: loading site script /usr/ports/Templates/config.site checking for gcc... cc 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 cc accepts -g... yes checking for cc option to enable C23 features... unsupported checking for cc option to enable C11 features... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for cc options to detect undeclared functions... -fno-builtin checking for cc options to ignore future-version functions... none needed checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) 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... no checking for cc option to support large files... none needed checking shared library type for unknown-FreeBSD... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... amd64-portbld-freebsd15.1 checking host system type... amd64-portbld-freebsd15.1 checking for getpagesize... (cached) yes checking for working mmap... (cached) yes checking for gmtime_r... yes checking for fsync... (cached) yes checking for drand48... yes checking for srand48_deterministic... no checking for getauxval... no checking for elf_aux_info... yes 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 log... -lm checking for zlib.h... (cached) 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 fstatat... yes checking for CMSG_LEN... yes checking for epoll... no checking for sendfile... yes, FreeBSD-style checking whether EHOSTDOWN is declared... yes checking whether ENONET is declared... no checking whether AI_V4MAPPED is declared... yes checking whether AI_ADDRCONFIG is declared... yes checking whether the compiler accepts -Wextra... yes checking whether the compiler accepts -Wformat... yes checking whether the compiler accepts -Wformat=2... yes checking whether the compiler accepts -Wconversion... yes checking whether the compiler accepts -Wtrampolines... no checking whether the compiler accepts -Wstrict-aliasing... yes checking whether the compiler accepts -fstack-clash-protection... yes checking whether the compiler accepts -fstack-protector-strong... yes checking whether the compiler accepts -fcf-protection=full... yes checking whether the compiler accepts -mbranch-protection=standard... no checking whether the compiler accepts -fno-delete-null-pointer-checks... yes checking whether the compiler accepts -Wl,-z,noexecstack... yes checking whether the compiler accepts -Wl,-z,relro... yes checking whether the compiler accepts -Wl,-z,now... yes checking whether the compiler accepts -Wl,--as-needed... yes checking whether the compiler accepts -Wl,--no-copy-dt-needed-entries... yes checking whether the compiler accepts -Wl,-z,nodlopen... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for htslib-1.23.1 cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o kfunc.o kfunc.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o kstring.o kstring.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o bcf_sr_sort.o bcf_sr_sort.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o bgzf.o bgzf.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o errmod.o errmod.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o faidx.o faidx.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o header.o header.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -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' \ 'cc' \ '-isystem /usr/local/include' \ '-Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden' \ '-Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden ' \ '-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto' > config_vars.h cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hts.o hts.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hts_expr.o hts_expr.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hts_os.o hts_os.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o md5.o md5.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o multipart.o multipart.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o probaln.o probaln.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o realn.o realn.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o regidx.o regidx.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o region.o region.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o sam.o sam.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o sam_mods.o sam_mods.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o simd.o simd.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o synced_bcf_reader.o synced_bcf_reader.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o vcf_sweep.o vcf_sweep.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o tbx.o tbx.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o textutils.o textutils.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o thread_pool.o thread_pool.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o vcf.o vcf.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o vcfutils.o vcfutils.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_codecs.o cram/cram_codecs.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_decode.o cram/cram_decode.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_encode.o cram/cram_encode.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_external.o cram/cram_external.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_index.o cram/cram_index.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_io.o cram/cram_io.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_stats.o cram/cram_stats.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/mFILE.o cram/mFILE.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/open_trace_file.o cram/open_trace_file.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/string_alloc.o cram/string_alloc.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -mavx2 -mpopcnt -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -mavx512f -mpopcnt -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hfile_libcurl.o hfile_libcurl.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hfile_gcs.o hfile_gcs.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hfile_s3.o hfile_s3.c ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o simd.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o hfile_gcs.o hfile_s3.o ranlib libhts.a cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o kfunc.pico kfunc.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o kstring.pico kstring.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o bgzf.pico bgzf.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o errmod.pico errmod.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o faidx.pico faidx.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o header.pico header.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hfile.pico hfile.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hts.pico hts.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hts_expr.pico hts_expr.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hts_os.pico hts_os.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o md5.pico md5.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o multipart.pico multipart.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o probaln.pico probaln.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o realn.pico realn.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o regidx.pico regidx.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o region.pico region.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o sam.pico sam.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o sam_mods.pico sam_mods.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o simd.pico simd.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o vcf_sweep.pico vcf_sweep.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o tbx.pico tbx.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o textutils.pico textutils.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o thread_pool.pico thread_pool.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o vcf.pico vcf.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o vcfutils.pico vcfutils.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_decode.pico cram/cram_decode.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_encode.pico cram/cram_encode.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_external.pico cram/cram_external.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_index.pico cram/cram_index.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_io.pico cram/cram_io.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_stats.pico cram/cram_stats.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/mFILE.pico cram/mFILE.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/string_alloc.pico cram/string_alloc.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -mavx2 -mpopcnt -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -mavx512f -mpopcnt -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hfile_libcurl.pico hfile_libcurl.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hfile_gcs.pico hfile_gcs.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hfile_s3.pico hfile_s3.c cc -shared -Wl,-soname,libhts.so.3 -Wl,-rpath,/usr/local/lib -L/usr/local/lib -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 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 hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread ln -sf libhts.so libhts.so.3 cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o annot-tsv.o annot-tsv.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o annot-tsv annot-tsv.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o bgzip.o bgzip.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htsfile.o htsfile.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o tabix.o tabix.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/hts_endian.o test/hts_endian.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/hts_endian test/hts_endian.o -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/fieldarith.o test/fieldarith.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/hfile.o test/hfile.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/pileup.o test/pileup.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/pileup_mod.o test/pileup_mod.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/plugins-dlhts.o test/plugins-dlhts.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/sam.o test/sam.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/sam test/sam.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_bgzf.o test/test_bgzf.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_expr.o test/test_expr.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_expr test/test_expr.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_faidx.o test/test_faidx.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_faidx test/test_faidx.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_kfunc.o test/test_kfunc.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_kfunc test/test_kfunc.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_khash.o test/test_khash.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_khash test/test_khash.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_kstring.o test/test_kstring.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_kstring test/test_kstring.o -lm cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_mod.o test/test_mod.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_mod test/test_mod.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_nibbles.o test/test_nibbles.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_nibbles test/test_nibbles.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_realn.o test/test_realn.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test-regidx.o test/test-regidx.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_str2int.o test/test_str2int.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_time_funcs.o test/test_time_funcs.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_time_funcs test/test_time_funcs.o cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_view.o test/test_view.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_index.o test/test_index.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test-vcf-api.o test/test-vcf-api.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test-bcf-sr.o test/test-bcf-sr.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test-bcf-translate.o test/test-bcf-translate.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test-parse-reg.o test/test-parse-reg.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test_introspection.o test/test_introspection.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread 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 cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/cmsg_wrap.o ref_cache/cmsg_wrap.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/http_parser.o ref_cache/http_parser.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/listener.o ref_cache/listener.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/log_files.o ref_cache/log_files.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/main.o ref_cache/main.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/misc.o ref_cache/misc.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/ping.o ref_cache/ping.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_epoll.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/poll_wrap_poll.o ref_cache/poll_wrap_poll.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/ref_files.o ref_cache/ref_files.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/request_handler.o ref_cache/request_handler.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/sendfile_wrap.o ref_cache/sendfile_wrap.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/server.o ref_cache/server.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/transaction.o ref_cache/transaction.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -isystem /usr/local/include -c -o ref_cache/upstream.o ref_cache/upstream.c cc -Wl,-rpath,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -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 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> htslib-1.23.1 depends on file: /usr/local/lib/libcrypto.so.12 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for htslib-1.23.1 ===> Generating temporary packing list mkdir -p -m 755 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/include /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/include/htslib /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/share/man/man1 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/share/man/man5 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/share/man/man7 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/pkgconfig if test -n ""; then mkdir -p -m 755 /wrkdirs/usr/ports/biology/htslib/work/stage; fi install -s -m 0644 libhts.so /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/libhts.so.1.23.1 ln -sf libhts.so.1.23.1 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/libhts.so ln -sf libhts.so.1.23.1 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/libhts.so.3 sed -e 's#@-includedir@#/usr/local/include#g;s#@-libdir@#/usr/local/lib#g;s#@-PACKAGE_VERSION@#1.23.1#g' htslib.pc.tmp > /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/pkgconfig/htslib.pc chmod 644 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/pkgconfig/htslib.pc install -s -m 555 annot-tsv bgzip htsfile tabix ref_cache/ref-cache /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/bin if test -n ""; then install -s -m 555 /wrkdirs/usr/ports/biology/htslib/work/stage; fi install -p -m 644 htslib/*.h /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/include/htslib install -p -m 644 libhts.a /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/libhts.a install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/share/man/man1 if test "xref_cache/ref-cache" != "x" ; then \ install -p -m 644 ref_cache/ref-cache.1 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/share/man/man1 ; \ fi install -p -m 644 faidx.5 sam.5 vcf.5 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/share/man/man7 ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-07-06T21:38:19+0000' 'PKG_NOTE_ports_top_git_hash=18628b9022c9c1c0e7cb5e71c2aa1e1e563ca34a' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=89c7d793da2638cfdc15252825a5548c3eb2f147' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.8' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for htslib-1.23.1 ===> Building htslib-1.23.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for htslib-1.23.1 build of biology/htslib | htslib-1.23.1 ended at Tue Jul 7 06:42:49 JST 2026 build time: 00:04:40