[package - main-amd64-default][biology/mothur] Failed for mothur-1.48.5 in build
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Date: Wed, 13 May 2026 05:35:36 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/beefy24/data/main-amd64-default/pe09c8d902664_sa3036edd029/logs/mothur-1.48.5.log
Build URL: https://pkg-status.freebsd.org/beefy24/build.html?mastername=main-amd64-default&build=pe09c8d902664_sa3036edd029
Log:
=>> Building biology/mothur
build started at Wed May 13 05:34:33 UTC 2026
port directory: /usr/ports/biology/mothur
package name: mothur-1.48.5
building for: FreeBSD main-amd64-default-job-27 16.0-CURRENT FreeBSD 16.0-CURRENT 1600018 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 867 Jan 22 01:01 /usr/ports/biology/mothur/Makefile
Ports top last git commit: e09c8d902664f49aa876230fa03a6d1228b9afa5
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: 27
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--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--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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BATCH=yes
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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) 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 (-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
===> mothur-1.48.5 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.7.5.pkg
[main-amd64-default-job-27] Installing pkg-2.7.5...
[main-amd64-default-job-27] 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-amd64-default-job-27] Installing bash-5.3.9...
[main-amd64-default-job-27] `-- Installing gettext-runtime-1.0_1...
[main-amd64-default-job-27] | `-- Installing indexinfo-0.3.1_1...
[main-amd64-default-job-27] | `-- Extracting indexinfo-0.3.1_1: .... done
[main-amd64-default-job-27] `-- Extracting gettext-runtime-1.0_1: .......... done
[main-amd64-default-job-27] 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-amd64-default-job-27] Installing gmake-4.4.1...
[main-amd64-default-job-27] 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_10.pkg
[main-amd64-default-job-27] Installing llvm15-15.0.7_10...
[main-amd64-default-job-27] `-- Installing libedit-3.1.20251016_1,1...
[main-amd64-default-job-27] `-- Extracting libedit-3.1.20251016_1,1: .......... done
[main-amd64-default-job-27] `-- Installing lua53-5.3.6_1...
[main-amd64-default-job-27] `-- Extracting lua53-5.3.6_1: .......... done
[main-amd64-default-job-27] `-- Installing perl5-5.42.2...
[main-amd64-default-job-27] `-- Extracting perl5-5.42.2: .......... done
<snip>
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:19:
In file included from /usr/include/c++/v1/__memory/shared_count.h:14:
In file included from /usr/include/c++/v1/typeinfo:392:
In file included from /usr/include/c++/v1/type_traits:528:
In file included from /usr/include/c++/v1/__type_traits/result_of.h:13:
In file included from /usr/include/c++/v1/__type_traits/invoke.h:21:
/usr/include/c++/v1/__type_traits/is_reference_wrapper.h:28:61: error: use of undeclared identifier '__remove_cv_t'
struct __is_reference_wrapper : __is_reference_wrapper_impl<__remove_cv_t<_Tp> > {};
^
/usr/include/c++/v1/__type_traits/make_unsigned.h:90:84: error: use of undeclared identifier '__make_unsigned_t'
using __copy_unsigned_t _LIBCPP_NODEBUG = __conditional_t<is_unsigned<_Tp>::value, __make_unsigned_t<_Up>, _Up>;
^
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:
In file included from /usr/include/c++/v1/tuple:225:
/usr/include/c++/v1/__memory/allocator_arg_t.h:42:37: error: 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:39:1: note: '__remove_const_t' declared here
using __remove_const_t = typename remove_const<_Tp>::type;
^
In file included from source/calculators/ace.cpp:10:
In file included from source/calculators/ace.h:16:
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:19:
In file included from /usr/include/c++/v1/__memory/shared_count.h:14:
In file included from /usr/include/c++/v1/typeinfo:392:
In file included from /usr/include/c++/v1/type_traits:528:
In file included from /usr/include/c++/v1/__type_traits/result_of.h:13:
In file included from /usr/include/c++/v1/__type_traits/invoke.h:21:
/usr/include/c++/v1/__type_traits/is_reference_wrapper.h:28:61: error: use of undeclared identifier '__remove_cv_t'
struct __is_reference_wrapper : __is_reference_wrapper_impl<__remove_cv_t<_Tp> > {};
^
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:
In file included from /usr/include/c++/v1/tuple:229:
/usr/include/c++/v1/__tuple/make_tuple_types.h:61:34: error: no template named '__remove_cvref_t'; did you mean '__remove_const_t'?
using _RawTp _LIBCPP_NODEBUG = __remove_cvref_t<_Tp>;
^
/usr/include/c++/v1/__type_traits/remove_const.h:39:1: note: '__remove_const_t' declared here
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: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:
In file included from /usr/include/c++/v1/tuple:225:
/usr/include/c++/v1/__memory/allocator_arg_t.h:42:37: error: 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:39:1: note: '__remove_const_t' declared here
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: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:
In file included from /usr/include/c++/v1/tuple:229:
/usr/include/c++/v1/__tuple/make_tuple_types.h:61:34: error: no template named '__remove_cvref_t'; did you mean '__remove_const_t'?
using _RawTp _LIBCPP_NODEBUG = __remove_cvref_t<_Tp>;
^
/usr/include/c++/v1/__type_traits/remove_const.h:39:1: note: '__remove_const_t' declared here
using __remove_const_t = typename remove_const<_Tp>::type;
^
In file included from source/calculators/ace.cpp:10:
In file included from source/calculators/ace.h:16:
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:
In file included from /usr/include/c++/v1/tuple:225:
/usr/include/c++/v1/__memory/allocator_arg_t.h:42:37: error: 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:39:1: note: '__remove_const_t' declared here
using __remove_const_t = typename remove_const<_Tp>::type;
^
In file included from source/calculators/ace.cpp:10:
In file included from source/calculators/ace.h:16:
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:
In file included from /usr/include/c++/v1/tuple:229:
/usr/include/c++/v1/__tuple/make_tuple_types.h:61:34: error: no template named '__remove_cvref_t'; did you mean '__remove_const_t'?
using _RawTp _LIBCPP_NODEBUG = __remove_cvref_t<_Tp>;
^
/usr/include/c++/v1/__type_traits/remove_const.h:39:1: note: '__remove_const_t' declared here
using __remove_const_t = typename remove_const<_Tp>::type;
^
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=]
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: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=]
In file included from source/calculators/ace.cpp:10:
In file included from source/calculators/ace.h:16:
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.
gmake: *** [Makefile:142: source/calculators/accuracy.o] Error 1
20 errors generated.
gmake: *** [Makefile:140: source/calculators/ace.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