[package - main-arm64-default][biology/mothur] Failed for mothur-1.48.5 in build
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Date: Mon, 01 Jun 2026 18:35:45 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: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/ampere2/data/main-arm64-default/p50aa2c1cc258_s5a8e0e03ae8/logs/mothur-1.48.5.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p50aa2c1cc258_s5a8e0e03ae8
Log:
=>> Building biology/mothur
build started at Mon Jun 1 18:35:31 UTC 2026
port directory: /usr/ports/biology/mothur
package name: mothur-1.48.5
building for: FreeBSD main-arm64-default-job-05 16.0-CURRENT FreeBSD 16.0-CURRENT 1600018 arm64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 867 Jan 29 01:03 /usr/ports/biology/mothur/Makefile
Ports top last git commit: 50aa2c1cc258dd977967f6babe3f9efd5038a269
Ports top unclean checkout: no
Port dir last git commit: 51eec7986b3681113cdef6be0a264a274eab0fc9
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.8
Host OSVERSION: 1600018
Jail OSVERSION: 1600018
Job Id: 05
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yuri@FreeBSD.org
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--CONFIGURE_ENV--
MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mothur/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mothur/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mothur/work/.cache HOME=/wrkdirs/usr/ports/biology/mothur/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mothur/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mothur/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
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lude -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"
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--End PLIST_SUB--
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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
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swap limit (kbytes, -w) unlimited
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pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
pipebuf (-y) unlimited
virtual machines (-V) 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
===> mothur-1.48.5 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.7.5.pkg
[main-arm64-default-job-05] Installing pkg-2.7.5...
[main-arm64-default-job-05] Extracting pkg-2.7.5: .......... done
===> mothur-1.48.5 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of mothur-1.48.5
===========================================================================
=======================<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 mothur-1.48.5 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 mothur-1.48.5 for building
=> SHA256 Checksum OK for mothur-mothur-v1.48.5_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 mothur-1.48.5 for building
===> Extracting for mothur-1.48.5
=> SHA256 Checksum OK for mothur-mothur-v1.48.5_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 mothur-1.48.5
===> Applying FreeBSD patches for mothur-1.48.5 from /usr/ports/biology/mothur/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> mothur-1.48.5 depends on executable: bash - not found
===> Installing existing package /packages/All/bash-5.3.9.pkg
[main-arm64-default-job-05] Installing bash-5.3.9...
[main-arm64-default-job-05] `-- Installing gettext-runtime-1.0_1...
[main-arm64-default-job-05] | `-- Installing indexinfo-0.3.1_1...
[main-arm64-default-job-05] | `-- Extracting indexinfo-0.3.1_1: .... done
[main-arm64-default-job-05] `-- Extracting gettext-runtime-1.0_1: .......... done
[main-arm64-default-job-05] Extracting bash-5.3.9: .......... done
===> mothur-1.48.5 depends on executable: bash - found
===> Returning to build of mothur-1.48.5
===> mothur-1.48.5 depends on package: gmake>=4.4.1 - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[main-arm64-default-job-05] Installing gmake-4.4.1...
[main-arm64-default-job-05] Extracting gmake-4.4.1: .......... done
===> mothur-1.48.5 depends on package: gmake>=4.4.1 - found
===> Returning to build of mothur-1.48.5
===> mothur-1.48.5 depends on executable: llvm-config15 - not found
===> Installing existing package /packages/All/llvm15-15.0.7_12.pkg
[main-arm64-default-job-05] Installing llvm15-15.0.7_12...
[main-arm64-default-job-05] `-- Installing libedit-3.1.20251016_1,1...
[main-arm64-default-job-05] `-- Extracting libedit-3.1.20251016_1,1: .......... done
[main-arm64-default-job-05] `-- Installing lua53-5.3.6_1...
[main-arm64-default-job-05] `-- Extracting lua53-5.3.6_1: .......... done
[main-arm64-default-job-05] `-- Installing perl5-5.42.2...
<snip>
In file included from In file included from In file included from /usr/include/c++/v1/iostream/usr/include/c++/v1/iostream/usr/include/c++/v1/iostream:::454545:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/ios/usr/include/c++/v1/ios/usr/include/c++/v1/ios:::228228228:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/__locale/usr/include/c++/v1/__locale/usr/include/c++/v1/__locale:::191919:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/__memory/shared_count.h/usr/include/c++/v1/__memory/shared_count.h/usr/include/c++/v1/__memory/shared_count.h:::141414:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/typeinfo/usr/include/c++/v1/typeinfo/usr/include/c++/v1/typeinfo:::392392392:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/type_traits/usr/include/c++/v1/type_traits/usr/include/c++/v1/type_traits:::528528528:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/__type_traits/result_of.h/usr/include/c++/v1/__type_traits/result_of.h/usr/include/c++/v1/__type_traits/result_of.h:::131313:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/__type_traits/invoke.h/usr/include/c++/v1/__type_traits/invoke.h/usr/include/c++/v1/__type_traits/invoke.h:::212121:
:
:
/usr/include/c++/v1/__type_traits/is_reference_wrapper.h/usr/include/c++/v1/__type_traits/is_reference_wrapper.h/usr/include/c++/v1/__type_traits/is_reference_wrapper.h:::282828:::616161::: error: error: error: use of undeclared identifier '__remove_cv_t'use of undeclared identifier '__remove_cv_t'use of undeclared identifier '__remove_cv_t'
struct __is_reference_wrapper : __is_reference_wrapper_impl<__remove_cv_t<_Tp> > {};struct __is_reference_wrapper : __is_reference_wrapper_impl<__remove_cv_t<_Tp> > {};
struct __is_reference_wrapper : __is_reference_wrapper_impl<__remove_cv_t<_Tp> > {};
^
^
^
In file included from In file included from source/calculators/ace.cppsource/calculators/bergerparker.cpp::1010:
:
In file included from In file included from In file included from source/calculators/accuracy.cppsource/calculators/ace.hsource/calculators/bergerparker.h:::91612:
:
:
In file included from In file included from In file included from source/calculators/accuracy.hppsource/calculators/calculator.hsource/calculators/calculator.h:::1255:
:
:
In file included from In file included from In file included from source/calculators/calculator.hsource/datastructures/sabundvector.hppsource/datastructures/sabundvector.hpp:::544:
:
:
In file included from In file included from In file included from source/datastructures/datavector.hppsource/datastructures/datavector.hppsource/datastructures/sabundvector.hpp:::444:
:
:
In file included from In file included from In file included from source/mothurout.hsource/mothurout.hsource/datastructures/datavector.hpp:::13134:
:
:
In file included from In file included from In file included from source/mothur.hsource/mothur.hsource/mothurout.h:::292913:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/iostream/usr/include/c++/v1/iostreamsource/mothur.h:::454529:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/ios/usr/include/c++/v1/ios/usr/include/c++/v1/iostream:::22822845:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/__locale/usr/include/c++/v1/__locale/usr/include/c++/v1/ios:::2020228:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/__mutex/once_flag.h/usr/include/c++/v1/__mutex/once_flag.h/usr/include/c++/v1/__locale:::222220:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/tuple/usr/include/c++/v1/tuple/usr/include/c++/v1/__mutex/once_flag.h:::22522522:
:
:
/usr/include/c++/v1/__memory/allocator_arg_t.h/usr/include/c++/v1/__memory/allocator_arg_t.hIn file included from ::/usr/include/c++/v1/tuple4242:::2253737:
::/usr/include/c++/v1/__memory/allocator_arg_t.h :error: error: 42no template named '__remove_cvref_t'; did you mean '__remove_const_t'?no template named '__remove_cvref_t'; did you mean '__remove_const_t'?:
37: error: using _RawAlloc _LIBCPP_NODEBUG = __remove_cvref_t<_Alloc>; using _RawAlloc _LIBCPP_NODEBUG = __remove_cvref_t<_Alloc>;no template named '__remove_cvref_t'; did you mean '__remove_const_t'?
^ ^
using _RawAlloc _LIBCPP_NODEBUG = __remove_cvref_t<_Alloc>;/usr/include/c++/v1/__type_traits/remove_const.h
/usr/include/c++/v1/__type_traits/remove_const.h: ^:39
39::/usr/include/c++/v1/__type_traits/remove_const.h11:::39 :note: note: 1'__remove_const_t' declared here'__remove_const_t' declared here:
note: '__remove_const_t' declared hereusing __remove_const_t = typename remove_const<_Tp>::type;
using __remove_const_t = typename remove_const<_Tp>::type;
using __remove_const_t = typename remove_const<_Tp>::type;
^
^
^
In file included from In file included from In file included from source/calculators/bergerparker.cppsource/calculators/ace.cppsource/calculators/accuracy.cpp:::10109:
:
:
In file included from In file included from In file included from source/calculators/bergerparker.hsource/calculators/ace.hsource/calculators/accuracy.hpp:::121612:
:
:
In file included from In file included from In file included from source/calculators/calculator.hsource/calculators/calculator.hsource/calculators/calculator.h:::555:
:
:
In file included from In file included from In file included from source/datastructures/sabundvector.hppsource/datastructures/sabundvector.hppsource/datastructures/sabundvector.hpp:::444:
:
:
In file included from In file included from In file included from source/datastructures/datavector.hppsource/datastructures/datavector.hppsource/datastructures/datavector.hpp:::444:
:
:
In file included from In file included from In file included from source/mothurout.hsource/mothurout.hsource/mothurout.h:::131313:
:
:
In file included from In file included from In file included from source/mothur.hsource/mothur.hsource/mothur.h:::292929:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/iostream/usr/include/c++/v1/iostream/usr/include/c++/v1/iostream:::454545:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/ios/usr/include/c++/v1/ios/usr/include/c++/v1/ios:::228228228:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/__locale/usr/include/c++/v1/__locale/usr/include/c++/v1/__locale:::202020:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/__mutex/once_flag.h/usr/include/c++/v1/__mutex/once_flag.h/usr/include/c++/v1/__mutex/once_flag.h:::222222:
:
:
In file included from In file included from In file included from /usr/include/c++/v1/tuple/usr/include/c++/v1/tuple/usr/include/c++/v1/tuple:::229229229:
:
:
/usr/include/c++/v1/__tuple/make_tuple_types.h/usr/include/c++/v1/__tuple/make_tuple_types.h/usr/include/c++/v1/__tuple/make_tuple_types.h:::616161:::343434::: error: error: error: no template named '__remove_cvref_t'; did you mean '__remove_const_t'?no template named '__remove_cvref_t'; did you mean '__remove_const_t'?no template named '__remove_cvref_t'; did you mean '__remove_const_t'?
using _RawTp _LIBCPP_NODEBUG = __remove_cvref_t<_Tp>; using _RawTp _LIBCPP_NODEBUG = __remove_cvref_t<_Tp>; using _RawTp _LIBCPP_NODEBUG = __remove_cvref_t<_Tp>;
^ ^ ^
/usr/include/c++/v1/__type_traits/remove_const.h/usr/include/c++/v1/__type_traits/remove_const.h:/usr/include/c++/v1/__type_traits/remove_const.h:39:39:39:1:1:1: : note: note: '__remove_const_t' declared herenote: '__remove_const_t' declared here
'__remove_const_t' declared here
using __remove_const_t = typename remove_const<_Tp>::type;
using __remove_const_t = typename remove_const<_Tp>::type;^
using __remove_const_t = typename remove_const<_Tp>::type;^
^
In file included from source/calculators/accuracy.cpp:9:
In file included from source/calculators/accuracy.hpp:12:
In file included from source/calculators/calculator.h:In file included from 5source/calculators/ace.cpp:
:In file included from 10source/datastructures/sabundvector.hpp:
:In file included from 4source/calculators/ace.h:
:In file included from 16source/datastructures/datavector.hpp:
:In file included from 4source/calculators/calculator.h:
:In file included from 5source/mothurout.h:
:In file included from 13source/datastructures/sabundvector.hpp:
:In file included from 4source/mothur.h:
:In file included from 29source/datastructures/datavector.hpp:
:In file included from 4/usr/include/c++/v1/iostream:
:In file included from 45source/mothurout.h:
:In file included from 13/usr/include/c++/v1/ios:
:In file included from 228source/mothur.h:
:In file included from 29/usr/include/c++/v1/__locale:
:In file included from 20/usr/include/c++/v1/iostream:
:In file included from 45/usr/include/c++/v1/__mutex/once_flag.h:
:In file included from 22/usr/include/c++/v1/ios:
:/usr/include/c++/v1/tuple228::
338In file included from :/usr/include/c++/v1/__locale37::20 :
error: In file included from use of undeclared identifier '__remove_cvref_t'/usr/include/c++/v1/__mutex/once_flag.h
:22:
/usr/include/c++/v1/tuple:338:37 __enable_if_t<_And<_IsNotSame<__remove_cvref_t<_Tp>, __tuple_leaf>, is_constructible<_Hp, _Tp> >::value, int> = 0>:
^error:
use of undeclared identifier '__remove_cvref_t'
fatal error: __enable_if_t<_And<_IsNotSame<__remove_cvref_t<_Tp>, __tuple_leaf>, is_constructible<_Hp, _Tp> >::value, int> = 0>too many errors emitted, stopping now [-ferror-limit=]
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
In file included from source/calculators/bergerparker.cpp:10:
In file included from source/calculators/bergerparker.h:12:
In file included from source/calculators/calculator.h:5:
In file included from source/datastructures/sabundvector.hpp:4:
In file included from source/datastructures/datavector.hpp:4:
In file included from source/mothurout.h:13:
In file included from source/mothur.h:29:
In file included from /usr/include/c++/v1/iostream:45:
In file included from /usr/include/c++/v1/ios:228:
In file included from /usr/include/c++/v1/__locale:20:
In file included from /usr/include/c++/v1/__mutex/once_flag.h:22:
/usr/include/c++/v1/tuple:338:37: error: use of undeclared identifier '__remove_cvref_t'
__enable_if_t<_And<_IsNotSame<__remove_cvref_t<_Tp>, __tuple_leaf>, is_constructible<_Hp, _Tp> >::value, int> = 0>
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
gmake: *** [Makefile:140: source/calculators/bergerparker.o] Error 1
gmake: *** Waiting for unfinished jobs....
20 errors generated.
20 errors generated.
gmake: *** [Makefile:140: source/calculators/ace.o] Error 1
gmake: *** [Makefile:142: source/calculators/accuracy.o] Error 1
===> 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/mothur