[package - main-armv7-default][biology/htslib] Failed for htslib-1.21 in build
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Date: Fri, 01 Nov 2024 10:27:30 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/ampere2/data/main-armv7-default/p711a2f7f1ca4_s0d965bc034/logs/htslib-1.21.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p711a2f7f1ca4_s0d965bc034
Log:
=>> Building biology/htslib
build started at Fri Nov 1 10:26:45 UTC 2024
port directory: /usr/ports/biology/htslib
package name: htslib-1.21
building for: FreeBSD main-armv7-default-job-11 15.0-CURRENT FreeBSD 15.0-CURRENT 1500026 arm
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1098 Oct 15 01:04 /usr/ports/biology/htslib/Makefile
Ports top last git commit: 711a2f7f1ca
Ports top unclean checkout: no
Port dir last git commit: aafe5d31c5f
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500023
Jail OSVERSION: 1500026
Job Id: 11
!!! Jail is newer than host. (Jail: 1500026, Host: 1500023) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1500026
UNAME_v=FreeBSD 15.0-CURRENT 1500026
UNAME_r=15.0-CURRENT
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=3.4.2
MASTERMNT=/usr/local/poudriere/data/.m/main-armv7-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/main-armv7-default/11/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-armv7-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-armv7-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.2
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-1.21:
CURL=on: Use libcurl for network file access (HTTPS and S3 support).
===> 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=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=2.72 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 OPENSSLDIR=/etc/ssl OPENSSLINC=/usr/include OPENSSLLIB=/usr/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=2.72 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=" -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protec
tor-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="1.21" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 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/5.36 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---
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
ulimit: can't get limit: Invalid argument
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 524288
stack size (kbytes, -s) 65536
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
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> htslib-1.21 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[main-armv7-default-job-11] Installing pkg-1.21.3...
[main-armv7-default-job-11] Extracting pkg-1.21.3: .......... done
===> htslib-1.21 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of htslib-1.21
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE MIT accepted by the user
===> Fetching all distfiles required by htslib-1.21 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE MIT accepted by the user
===> Fetching all distfiles required by htslib-1.21 for building
=> SHA256 Checksum OK for htslib-1.21.tar.bz2.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE MIT accepted by the user
===> Fetching all distfiles required by htslib-1.21 for building
===> Extracting for htslib-1.21
=> SHA256 Checksum OK for htslib-1.21.tar.bz2.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for htslib-1.21
===> Applying FreeBSD patches for htslib-1.21 from /usr/ports/biology/htslib/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> htslib-1.21 depends on package: gmake>=4.4.1 - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[main-armv7-default-job-11] Installing gmake-4.4.1...
[main-armv7-default-job-11] `-- Installing gettext-runtime-0.22.5...
[main-armv7-default-job-11] | `-- Installing indexinfo-0.3.1...
<snip>
[main-armv7-default-job-11] `-- Installing m4-1.4.19_1,1...
[main-armv7-default-job-11] `-- Extracting m4-1.4.19_1,1: .......... done
[main-armv7-default-job-11] `-- Installing perl5-5.36.3_2...
[main-armv7-default-job-11] `-- Extracting perl5-5.36.3_2: .......... done
[main-armv7-default-job-11] Extracting autoconf-2.72: .......... done
===> htslib-1.21 depends on package: autoconf>=2.72 - found
===> Returning to build of htslib-1.21
===> htslib-1.21 depends on package: automake>=1.17 - not found
===> Installing existing package /packages/All/automake-1.17.pkg
[main-armv7-default-job-11] Installing automake-1.17...
[main-armv7-default-job-11] Extracting automake-1.17: .......... done
===> htslib-1.21 depends on package: automake>=1.17 - found
===> Returning to build of htslib-1.21
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> htslib-1.21 depends on shared library: libdeflate.so - not found
===> Installing existing package /packages/All/libdeflate-1.22.pkg
[main-armv7-default-job-11] Installing libdeflate-1.22...
[main-armv7-default-job-11] Extracting libdeflate-1.22: .......... done
===> htslib-1.21 depends on shared library: libdeflate.so - found (/usr/local/lib/libdeflate.so)
===> Returning to build of htslib-1.21
===> htslib-1.21 depends on shared library: libcurl.so - not found
===> Installing existing package /packages/All/curl-8.10.1.pkg
[main-armv7-default-job-11] Installing curl-8.10.1...
[main-armv7-default-job-11] `-- Installing libnghttp2-1.63.0...
[main-armv7-default-job-11] `-- Extracting libnghttp2-1.63.0: .......... done
[main-armv7-default-job-11] `-- Installing libpsl-0.21.5_1...
[main-armv7-default-job-11] | `-- Installing libidn2-2.3.7...
[main-armv7-default-job-11] | | `-- Installing libunistring-1.2...
[main-armv7-default-job-11] | | `-- Extracting libunistring-1.2: .......... done
[main-armv7-default-job-11] | `-- Extracting libidn2-2.3.7: .......... done
[main-armv7-default-job-11] `-- Extracting libpsl-0.21.5_1: .......... done
[main-armv7-default-job-11] `-- Installing libssh2-1.11.0_1,3...
[main-armv7-default-job-11] `-- Extracting libssh2-1.11.0_1,3: .......... done
[main-armv7-default-job-11] Extracting curl-8.10.1: .......... done
===> htslib-1.21 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so)
===> Returning to build of htslib-1.21
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for htslib-1.21
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 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 needed to detect all undeclared functions... -fno-builtin
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... no
checking whether __cpuid_count is declared... no
checking for pkg-config... no
checking for cc option to enable large file support... 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... armv7-portbld-freebsd15.0
checking host system type... armv7-portbld-freebsd15.0
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 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 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
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for htslib-1.21
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 "1.21"' > 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' \
'-fstack-protector-strong -fvisibility=hidden ' \
'-ldeflate -llzma -lbz2 -lz -lm -L/usr/local/lib -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_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 -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
htscodecs/htscodecs/rANS_static4x16pr.c:1073:19: error: use of undeclared identifier 'rans_compress_O1_32x16_neon'; did you mean 'rans_compress_O1_32x16'?
1073 | ? rans_compress_O1_32x16_neon
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| rans_compress_O1_32x16
htscodecs/htscodecs/rANS_static32x16pr.h:70:16: note: 'rans_compress_O1_32x16' declared here
70 | unsigned char *rans_compress_O1_32x16(unsigned char *in,
| ^
htscodecs/htscodecs/rANS_static4x16pr.c:1074:19: error: use of undeclared identifier 'rans_compress_O0_32x16_neon'; did you mean 'rans_compress_O0_32x16'?
1074 | : rans_compress_O0_32x16_neon;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| rans_compress_O0_32x16
htscodecs/htscodecs/rANS_static32x16pr.h:60:16: note: 'rans_compress_O0_32x16' declared here
60 | unsigned char *rans_compress_O0_32x16(unsigned char *in,
| ^
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_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
htscodecs/htscodecs/rANS_static4x16pr.c:1096:19: error: use of undeclared identifier 'rans_uncompress_O1_32x16_neon'; did you mean 'rans_uncompress_O1_32x16'?
1096 | ? rans_uncompress_O1_32x16_neon
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| rans_uncompress_O1_32x16
htscodecs/htscodecs/rANS_static32x16pr.h:75:16: note: 'rans_uncompress_O1_32x16' declared here
75 | unsigned char *rans_uncompress_O1_32x16(unsigned char *in,
| ^
htscodecs/htscodecs/rANS_static4x16pr.c:1097:19: error: use of undeclared identifier 'rans_uncompress_O0_32x16_neon'; did you mean 'rans_uncompress_O0_32x16'?
1097 | : rans_uncompress_O0_32x16_neon;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| rans_uncompress_O0_32x16
htscodecs/htscodecs/rANS_static32x16pr.h:65:16: note: 'rans_uncompress_O0_32x16' declared here
65 | unsigned char *rans_uncompress_O0_32x16(unsigned char *in,
| ^
4 errors generated.
gmake: *** [Makefile:194: htscodecs/htscodecs/rANS_static4x16pr.o] Error 1
gmake: *** Waiting for unfinished jobs....
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped making "build" in /usr/ports/biology/htslib