[package - main-arm64-default][biology/vsearch] Failed for vsearch-2.30.2 in build
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Date: Fri, 02 Jan 2026 08:50:14 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-arm64-default/pa7ae0233f66f_s7f39d05b67a/logs/vsearch-2.30.2.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=pa7ae0233f66f_s7f39d05b67a
Log:
=>> Building biology/vsearch
build started at Fri Jan 2 08:49:29 -00 2026
port directory: /usr/ports/biology/vsearch
package name: vsearch-2.30.2
building for: FreeBSD main-arm64-default-job-08 16.0-CURRENT FreeBSD 16.0-CURRENT 1600007 arm64
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 650 Dec 20 01:04 /usr/ports/biology/vsearch/Makefile
Ports top last git commit: a7ae0233f66f482aa49743f371c73aa581777b5c
Ports top unclean checkout: no
Port dir last git commit: be3bc42e2e6d287eccd8c58797e3bce89d7f82fc
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.4-15-g61aba751
Host OSVERSION: 1600000
Jail OSVERSION: 1600007
Job Id: 08
!!! Jail is newer than host. (Jail: 1600007, Host: 1600000) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1600007
UNAME_v=FreeBSD 16.0-CURRENT 1600007
UNAME_r=16.0-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=3.4.4-15-g61aba751
MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-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-arm64-default/08/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-arm64-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.4-15-g61aba751
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 vsearch-2.30.2:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vsearch/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vsearch/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vsearch/work/.cache HOME=/wrkdirs/usr/ports/biology/vsearch/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vsearch/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vsearch/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--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vsearch/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vsearch/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vsearch/work/.cache HOME=/wrkdirs/usr/ports/biology/vsearch/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vsearch/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vsearch/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=" " LIBS="-L/usr/local/lib" 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--
PORTDOCS="" DOCS="" NO_DOCS="@comment " OSREL=16.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/vsearch" EXAMPLESDIR="share/examples/vsearch" DATADIR="share/vsearch" WWWDIR="www/vsearch" ETCDIR="etc/vsearch"
--End PLIST_SUB--
--SUB_LIST--
DOCS="" NO_DOCS="@comment " PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vsearch DOCSDIR=/usr/local/share/doc/vsearch EXAMPLESDIR=/usr/local/share/examples/vsearch WWWDIR=/usr/local/www/vsearch ETCDIR=/usr/local/etc/vsearch
--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--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 1048576
stack size (kbytes, -s) 1048576
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 (-y) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> vsearch-2.30.2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.5.0.pkg
[main-arm64-default-job-08] Installing pkg-2.5.0...
[main-arm64-default-job-08] Extracting pkg-2.5.0: .......... done
===> vsearch-2.30.2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of vsearch-2.30.2
===========================================================================
=======================<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 GPLv3 accepted by the user
===> Fetching all distfiles required by vsearch-2.30.2 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by vsearch-2.30.2 for building
=> SHA256 Checksum OK for torognes-vsearch-v2.30.2_GH0.tar.gz.
===========================================================================
=======================<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 GPLv3 accepted by the user
===> Fetching all distfiles required by vsearch-2.30.2 for building
===> Extracting for vsearch-2.30.2
=> SHA256 Checksum OK for torognes-vsearch-v2.30.2_GH0.tar.gz.
===========================================================================
=======================<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 vsearch-2.30.2
===> Applying FreeBSD patches for vsearch-2.30.2 from /usr/ports/biology/vsearch/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> vsearch-2.30.2 depends on package: ghostscript10>=10.02.0 - not found
===> Installing existing package /packages/All/ghostscript10-10.06.0_1.pkg
[main-arm64-default-job-08] Installing ghostscript10-10.06.0_1...
[main-arm64-default-job-08] `-- Installing cups-2.4.16...
[main-arm64-default-job-08] | `-- Installing avahi-app-0.8_6...
<snip>
The environment variable "FREETYPE_PROPERTIES" can be used to control the
driver properties. Example:
FREETYPE_PROPERTIES=truetype:interpreter-version=35 \
cff:no-stem-darkening=1 \
autofitter:warping=1
This allows to select, say, the subpixel hinting mode at runtime for a given
application.
If LONG_PCF_NAMES port's option was enabled, the PCF family names may include
the foundry and information whether they contain wide characters. For example,
"Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at
run time with using pcf:no-long-family-names property, if needed. Example:
FREETYPE_PROPERTIES=pcf:no-long-family-names=1
How to recreate fontconfig cache with using such environment variable,
if needed:
# env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv
The controllable properties are listed in the section "Controlling FreeType
Modules" in the reference's table of contents
(/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed).
=====
Message from ghostscript10-10.06.0_1:
--
This package installs a script named dvipdf that depends on dvips. If you
want to use this script you need to install print/tex-dvipsk.
===> vsearch-2.30.2 depends on package: ghostscript10>=10.02.0 - found
===> Returning to build of vsearch-2.30.2
===> vsearch-2.30.2 depends on package: gmake>=4.4.1 - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[main-arm64-default-job-08] Installing gmake-4.4.1...
[main-arm64-default-job-08] Extracting gmake-4.4.1: .......... done
===> vsearch-2.30.2 depends on package: gmake>=4.4.1 - found
===> Returning to build of vsearch-2.30.2
===> vsearch-2.30.2 depends on package: autoconf>=2.72_1 - not found
===> Installing existing package /packages/All/autoconf-2.72_1.pkg
[main-arm64-default-job-08] Installing autoconf-2.72_1...
[main-arm64-default-job-08] `-- Installing autoconf-switch-20220527...
[main-arm64-default-job-08] `-- Extracting autoconf-switch-20220527: .......... done
[main-arm64-default-job-08] `-- Installing m4-1.4.20,1...
[main-arm64-default-job-08] `-- Extracting m4-1.4.20,1: .......... done
[main-arm64-default-job-08] `-- Installing perl5-5.42.0_1...
[main-arm64-default-job-08] `-- Extracting perl5-5.42.0_1: .......... done
[main-arm64-default-job-08] Extracting autoconf-2.72_1: .......... done
===> vsearch-2.30.2 depends on package: autoconf>=2.72_1 - found
===> Returning to build of vsearch-2.30.2
===> vsearch-2.30.2 depends on package: automake>=1.18.1 - not found
===> Installing existing package /packages/All/automake-1.18.1.pkg
[main-arm64-default-job-08] Installing automake-1.18.1...
[main-arm64-default-job-08] Extracting automake-1.18.1: .......... done
===> vsearch-2.30.2 depends on package: automake>=1.18.1 - found
===> Returning to build of vsearch-2.30.2
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for vsearch-2.30.2
configure.ac:103: installing './compile'
configure.ac:6: installing './config.guess'
configure.ac:6: installing './config.sub'
configure.ac:7: installing './install-sh'
configure.ac:7: installing './missing'
src/Makefile.am: installing './depcomp'
configure: loading site script /usr/ports/Templates/config.site
checking build system type... aarch64-portbld-freebsd16.0
checking host system type... aarch64-portbld-freebsd16.0
checking target system type... aarch64-portbld-freebsd16.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
checking whether build environment is sane... yes
checking for a race-free mkdir -p... (cached) /bin/mkdir -p
checking for gawk... (cached) /usr/bin/awk
checking whether /usr/local/bin/gmake sets $(MAKE)... yes
checking whether /usr/local/bin/gmake supports nested variables... yes
checking xargs -n works... yes
checking whether UID '0' is supported by ustar format... yes
checking whether GID '0' is supported by ustar format... yes
checking how to create a ustar tar archive... (cached) /usr/bin/tar
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 c++ accepts -g... yes
checking for c++ option to enable C++11 features... none needed
checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style)
checking dependency style of c++... gcc3
checking for ranlib... ranlib
checking for pthread_create in -lpthread... yes
checking for dlopen in -ldl... yes
checking for GetProcessMemoryInfo in -lpsapi... no
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 getopt.h... (cached) yes
checking for fcntl.h... (cached) yes
checking for regex.h... yes
checking for string.h... (cached) yes
checking for sys/time.h... (cached) yes
checking for dlfcn.h... (cached) yes
checking for pthread.h... (cached) yes
checking for inline... inline
checking for size_t... (cached) yes
checking for uint32_t... (cached) yes
checking for int64_t... (cached) yes
checking for uint64_t... (cached) yes
checking for uint8_t... (cached) yes
checking for memmove... (cached) yes
checking for memcpy... (cached) yes
checking for posix_memalign... yes
checking for gettimeofday... (cached) yes
checking for localtime... (cached) yes
checking for memchr... (cached) yes
checking for memset... (cached) yes
checking for pow... yes
checking for regcomp... yes
checking for strchr... (cached) yes
checking for strcspn... (cached) yes
checking for sysinfo... no
checking for bzlib.h... yes
checking for zlib.h... (cached) yes
checking for ps2pdf... yes
checking for windows.h... no
checking for gcc... cc
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 whether cc understands -c and -o together... yes
checking dependency style of cc... gcc3
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating man/Makefile
config.status: creating config.h
config.status: executing depfiles commands
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for vsearch-2.30.2
/usr/local/bin/gmake all-recursive
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.2'
Making all in src
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.2/src'
depbase=`echo align_simd.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -march=armv8-a+simd -mtune=generic -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT align_simd.o -MD -MP -MF $depbase.Tpo -c -o align_simd.o align_simd.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo allpairs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -march=armv8-a+simd -mtune=generic -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT allpairs.o -MD -MP -MF $depbase.Tpo -c -o allpairs.o allpairs.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo arch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -march=armv8-a+simd -mtune=generic -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT arch.o -MD -MP -MF $depbase.Tpo -c -o arch.o arch.cc &&\
mv -f $depbase.Tpo $depbase.Po
arch.cc:70:16: error: redefinition of 'memalignment' as different kind of symbol
70 | constexpr auto memalignment = 16;
| ^
/usr/include/stdlib.h:175:8: note: previous definition is here
175 | size_t memalignment(const void *) __pure2;
| ^
arch.cc:228:7: error: no matching function for call to 'posix_memalign'
228 | if (posix_memalign(&ptr, memalignment, size) != 0)
| ^~~~~~~~~~~~~~
/usr/include/stdlib.h:188:6: note: candidate function not viable: no known conversion from 'size_t (const void *)' (aka 'unsigned long (const void *)') to 'size_t' (aka 'unsigned long') for 2nd argument
188 | int posix_memalign(void **, size_t, size_t); /* (ADV) */
| ^ ~~~~~~
2 errors generated.
gmake[2]: *** [Makefile:859: arch.o] Error 1
gmake[2]: *** Waiting for unfinished jobs....
align_simd.cc:1420:8: warning: compound literals are a C99-specific feature [-Wc99-extensions]
1420 | T0 = v_init(-1, 0, 0, 0, 0, 0, 0, 0);
| ^
align_simd.cc:160:33: note: expanded from macro 'v_init'
160 | #define v_init(a,b,c,d,e,f,g,h) (const VECTOR_SHORT){a,b,c,d,e,f,g,h}
| ^
1 warning generated.
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.2/src'
gmake[1]: *** [Makefile:381: all-recursive] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.2'
gmake: *** [Makefile:322: all] Error 2
===> 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/vsearch