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Maintainer: [email protected] 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: [email protected] 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 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1600018 UNAME_v=FreeBSD 16.0-CURRENT 1600018 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=3.4.8 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/05/.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-3.4.8 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--- ---End OPTIONS List--- --MAINTAINER-- [email protected] --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" --End CONFIGURE_ENV-- --MAKE_ENV-- 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 MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="/usr/local/llvm15/bin/clang" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="/usr/local/llvm15/bin/clang-cpp" CPPFLAGS="-I/usr/local/include -isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="-L/usr/local/lib" CXX="/usr/local/llvm15/bin/clang++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/inc 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" --End MAKE_ENV-- --PLIST_SUB-- OSREL=16.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/mothur" EXAMPLESDIR="share/examples/mothur" DATADIR="share/mothur" WWWDIR="www/mothur" ETCDIR="etc/mothur" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mothur DOCSDIR=/usr/local/share/doc/mothur EXAMPLESDIR=/usr/local/share/examples/mothur WWWDIR=/usr/local/www/mothur ETCDIR=/usr/local/etc/mothur --End SUB_LIST-- ---Begin make.conf--- 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 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
