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Maintainer: [email protected] 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: [email protected] 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 ---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-amd64-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-amd64-default/27/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-amd64-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) 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
