From nobody Sat Dec 16 23:04:49 2023 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4St1rK6kn2z52sCG for ; Sat, 16 Dec 2023 23:04:49 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4St1rK24Jlz3GGV for ; Sat, 16 Dec 2023 23:04:49 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1702767889; a=rsa-sha256; cv=none; b=OC8JiVcwHcAsxYZQfFfTZOkdYSztgJNyVv8earE/6G2HaqF41rg0TcwYTM6RHXCF1WlZWF WDsho8XmOSzov54oWJdjv0mM9g/TgukYBD4s8IsbtNzI5E8Nc4UsbZ4M+8255yogHZVYg5 rPzrMDvpDWuQW7a7zxDs8a3zbNRcBmA+wRepNiSzgj6z0g7TKU2ZJaG7d6/AJiyJMI8ad4 JyssJUsrcKfsn46H5Ey8fV64LqYoRsNmV3fz9iOTsioU2WXr1ysfTaSZ8cS2aDJcwWeX6x N7v26dn81y7tFWtpDjhG19WkAiPSITyFTrCFk4FUbMI6yEr5udTfkB3JHOT2/g== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1702767889; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=NIp7yxnsKYw8uxgw6CQezFdlpWUllon7V4YeSepV8YE=; b=c0G8KvBbfniLJQkSsBGsperdNeCjFj1rvhtJS0bSACFG/fPKnZ3+1l897pKOgluyqq9hGQ OR0jIQIekvN30mpziI8kaoTKn4hISJuMEwPAb1GqBq8sRPLOP7Ze2T8Ezme6lbRx/BcRbu EguK0i5DlQtTsotmTPJanx46/Z7m12xmJImviDdtTX3xzda9MivAx+aXAKKCw6lexHuSp+ n6S5liENwqsmcbNbN4A8oSD2GuPjhkGokkIOBZCebbO0UCbQFmeZkCoAzyT9ganMLeZu+m sGsJlaPFSDg2+FJztKmulNmnUhU0+kvKLEQFcHIBtCNvmMudYHApkGlmCttllg== Received: from beefy18.nyi.freebsd.org (beefy18.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:21]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4St1rK0z6Tz1CPj for ; Sat, 16 Dec 2023 23:04:49 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 11b2 by beefy18.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy18.nyi.freebsd.org); Sat, 16 Dec 2023 23:04:49 +0000 To: jrm@FreeBSD.org Subject: [package - main-amd64-default][biology/diamond] Failed for diamond-2.1.8 in build Cc: pkg-fallout@FreeBSD.org Date: Sat, 16 Dec 2023 23:04:49 +0000 Message-Id: <657e2d11.11b2.184154de@beefy18.nyi.freebsd.org> From: List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org 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: jrm@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p1dd4264fe4a8_s59dba901f2/logs/diamond-2.1.8.log Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p1dd4264fe4a8_s59dba901f2 Log: =>> Building biology/diamond build started at Sat Dec 16 23:00:18 UTC 2023 port directory: /usr/ports/biology/diamond package name: diamond-2.1.8 building for: FreeBSD main-amd64-default-job-12 15.0-CURRENT FreeBSD 15.0-CURRENT 1500007 amd64 maintained by: jrm@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 414 Jul 11 01:01 /usr/ports/biology/diamond/Makefile Ports top last git commit: 1dd4264fe4a Ports top unclean checkout: no Port dir last git commit: 371eba15ec7 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.0 Host OSVERSION: 1500006 Jail OSVERSION: 1500007 Job Id: 12 !!! Jail is newer than host. (Jail: 1500007, Host: 1500006) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500007 UNAME_v=FreeBSD 15.0-CURRENT 1500007 UNAME_r=15.0-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=3.4.0 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/12/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS 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-3.4.0 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-- jrm@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/diamond/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/diamond/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/diamond/work/.cache HOME=/wrkdirs/usr/ports/biology/diamond/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/diamond/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/diamond/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/diamond/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/diamond/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/diamond/work/.cache HOME=/wrkdirs/usr/ports/biology/diamond/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/diamond/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/diamond/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 DESTDIR=/wrkdirs/usr/ports/biology/diamond/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTA LL_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-- CMAKE_BUILD_TYPE="release" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/diamond" EXAMPLESDIR="share/examples/diamond" DATADIR="share/diamond" WWWDIR="www/diamond" ETCDIR="etc/diamond" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/diamond DOCSDIR=/usr/local/share/doc/diamond EXAMPLESDIR=/usr/local/share/examples/diamond WWWDIR=/usr/local/www/diamond ETCDIR=/usr/local/etc/diamond --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 --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> diamond-2.1.8 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9.pkg [main-amd64-default-job-12] Installing pkg-1.20.9... [main-amd64-default-job-12] Extracting pkg-1.20.9: .......... done ===> diamond-2.1.8 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of diamond-2.1.8 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by diamond-2.1.8 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by diamond-2.1.8 for building => SHA256 Checksum OK for bbuchfink-diamond-v2.1.8_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by diamond-2.1.8 for building ===> Extracting for diamond-2.1.8 => SHA256 Checksum OK for bbuchfink-diamond-v2.1.8_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for diamond-2.1.8 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> diamond-2.1.8 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.27.9.pkg [main-amd64-default-job-12] Installing cmake-core-3.27.9... [main-amd64-default-job-12] `-- Installing expat-2.5.0... [main-amd64-default-job-12] `-- Extracting expat-2.5.0: .......... done [main-amd64-default-job-12] `-- Installing jsoncpp-1.9.5... [main-amd64-default-job-12] `-- Extracting jsoncpp-1.9.5: .......... done [main-amd64-default-job-12] `-- Installing libuv-1.47.0... [main-amd64-default-job-12] `-- Extracting libuv-1.47.0: .......... done [main-amd64-default-job-12] `-- Installing rhash-1.4.4... [main-amd64-default-job-12] | `-- Installing gettext-runtime-0.22.3... [main-amd64-default-job-12] | | `-- Installing indexinfo-0.3.1... [main-amd64-default-job-12] | | `-- Extracting indexinfo-0.3.1: .... done [main-amd64-default-job-12] | `-- Extracting gettext-runtime-0.22.3: .......... done [main-amd64-default-job-12] `-- Extracting rhash-1.4.4: .......... done [main-amd64-default-job-12] Extracting cmake-core-3.27.9: .......... done ===> diamond-2.1.8 depends on file: /usr/local/bin/cmake - found In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/global_ranking.h:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../output/output.h:25: In file included from /usr/include/c++/v1/map:2529: In file included from /usr/include/c++/v1/functional:526: In file included from /usr/include/c++/v1/__functional/boyer_moore_searcher.h:25: In file included from /usr/include/c++/v1/array:547: In file included from /usr/include/c++/v1/algorithm:1803: In file included from /usr/include/c++/v1/__algorithm/nth_element.h:15: /usr/include/c++/v1/__algorithm/sort.h:453:9: error: no viable overloaded '-=' 453 | __lm1 -= (__right_bitset == 0) ? __r_size : 0; | ~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/sort.h:568:8: note: in instantiation of function template specialization 'std::__bitset_partition_partial_blocks::Iterator, Search::Hit>' requested here 568 | std::__bitset_partition_partial_blocks<_AlgPolicy, _Compare>( | ^ /usr/include/c++/v1/__algorithm/sort.h:802:20: note: in instantiation of function template specialization 'std::__bitset_partition::Iterator, Search::Hit::CmpSubject &>' requested here 802 | ? std::__bitset_partition<_AlgPolicy, _RandomAccessIterator, _Compare>(__first, __last, __comp) | ^ /usr/include/c++/v1/__algorithm/sort.h:878:8: note: in instantiation of function template specialization 'std::__introsort::Iterator, false>' requested here 878 | std::__introsort<_AlgPolicy, | ^ /usr/include/c++/v1/__algorithm/sort.h:946:10: note: in instantiation of function template specialization 'std::__sort_dispatch::Iterator, Search::Hit::CmpSubject>' requested here 946 | std::__sort_dispatch<_AlgPolicy>(std::__unwrap_iter(__first), std::__unwrap_iter(__last), __comp); | ^ /usr/include/c++/v1/__algorithm/sort.h:954:8: note: in instantiation of function template specialization 'std::__sort_impl::Iterator, Search::Hit::CmpSubject>' requested here 954 | std::__sort_impl<_ClassicAlgPolicy>(std::move(__first), std::move(__last), __comp); | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../load_hits.h:44:7: note: in instantiation of function template specialization 'std::sort::Iterator, Search::Hit::CmpSubject>' requested here 44 | std::sort(begin, end, Search::Hit::CmpSubject()); | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/table.cpp:124:40: note: in instantiation of function template specialization 'Extension::load_hits::Iterator>' requested here 124 | Extension::SeedHitList l = Extension::load_hits(begin, end, cfg.target->seqs()); | ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/table.cpp:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/global_ranking.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../target.h:35: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/flat_array.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/ips4o.hpp:47: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/memory.hpp:50: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/buffers.hpp:65:55: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] 65 | static constexpr const bool kInitializedStorage = IS_TRIVIALLY_DEFAULT_CONSTRUCTIBLE(value_type); | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/buffers.hpp:45:47: note: expanded from macro 'IS_TRIVIALLY_DEFAULT_CONSTRUCTIBLE' 45 | #define IS_TRIVIALLY_DEFAULT_CONSTRUCTIBLE(T) __has_trivial_constructor(T) | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/buffers.hpp:139:52: note: in instantiation of static data member 'ips4o::detail::Sorter::Iterator, Search::Hit::CmpQueryTarget>>::Block::kInitializedStorage' requested here 139 | using storage_type = typename std::conditional::Iterator, Search::Hit::CmpQueryTarget>>::Block' requested here 230 | static_assert(sizeof(Block) == sizeof(typename Cfg::value_type) * Cfg::kBlockSize, "Block size mismatch."); | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/memory.hpp:174:13: note: in instantiation of member class 'ips4o::detail::Sorter::Iterator, Search::Hit::CmpQueryTarget>>::Buffers' requested here 174 | Buffers buffers; | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/memory.hpp:76:31: note: in instantiation of member class 'ips4o::detail::Sorter::Iterator, Search::Hit::CmpQueryTarget>>::LocalData' requested here 76 | : alloc_(new char[sizeof(T) + alignment]) | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/sequential.hpp:102:15: note: in instantiation of function template specialization 'ips4o::detail::AlignedPtr::Iterator, Search::Hit::CmpQueryTarget>>::LocalData>::AlignedPtr' requested here 102 | , local_ptr_(Cfg::kDataAlignment, std::move(comp), buffer_storage_.get()) {} | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/ips4o.hpp:71:67: note: in instantiation of member function 'ips4o::SequentialSorter::Iterator, Search::Hit::CmpQueryTarget>>::SequentialSorter' requested here 71 | ips4o::SequentialSorter> sorter{false, std::move(comp)}; | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/ips4o.hpp:128:16: note: in instantiation of function template specialization 'ips4o::sort, Deque::Iterator, Search::Hit::CmpQueryTarget>' requested here 128 | ips4o::sort(std::move(begin), std::move(end), std::move(comp)); | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/table.cpp:159:19: note: in instantiation of function template specialization 'ips4o::parallel::sort, Deque::Iterator, Search::Hit::CmpQueryTarget>' requested here 159 | ips4o::parallel::sort(hits.begin(), hits.end(), Search::Hit::CmpQueryTarget(), config.threads_); | ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/table.cpp:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/global_ranking.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../target.h:35: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/flat_array.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/ips4o.hpp:47: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/memory.hpp:50: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/buffers.hpp:231:19: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] 231 | static_assert(IS_TRIVIALLY_DEFAULT_CONSTRUCTIBLE(Block), "Block must be trivially default constructible."); | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/buffers.hpp:45:47: note: expanded from macro 'IS_TRIVIALLY_DEFAULT_CONSTRUCTIBLE' 45 | #define IS_TRIVIALLY_DEFAULT_CONSTRUCTIBLE(T) __has_trivial_constructor(T) | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/memory.hpp:174:13: note: in instantiation of member class 'ips4o::detail::Sorter::Iterator, Search::Hit::CmpQueryTarget>>::Buffers' requested here 174 | Buffers buffers; | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/memory.hpp:76:31: note: in instantiation of member class 'ips4o::detail::Sorter::Iterator, Search::Hit::CmpQueryTarget>>::LocalData' requested here 76 | : alloc_(new char[sizeof(T) + alignment]) | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/sequential.hpp:102:15: note: in instantiation of function template specialization 'ips4o::detail::AlignedPtr::Iterator, Search::Hit::CmpQueryTarget>>::LocalData>::AlignedPtr' requested here 102 | , local_ptr_(Cfg::kDataAlignment, std::move(comp), buffer_storage_.get()) {} | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/ips4o.hpp:71:67: note: in instantiation of member function 'ips4o::SequentialSorter::Iterator, Search::Hit::CmpQueryTarget>>::SequentialSorter' requested here 71 | ips4o::SequentialSorter> sorter{false, std::move(comp)}; | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/ips4o.hpp:128:16: note: in instantiation of function template specialization 'ips4o::sort, Deque::Iterator, Search::Hit::CmpQueryTarget>' requested here 128 | ips4o::sort(std::move(begin), std::move(end), std::move(comp)); | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/table.cpp:159:19: note: in instantiation of function template specialization 'ips4o::parallel::sort, Deque::Iterator, Search::Hit::CmpQueryTarget>' requested here 159 | ips4o::parallel::sort(hits.begin(), hits.end(), Search::Hit::CmpQueryTarget(), config.threads_); | ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/table.cpp:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/global_ranking.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../target.h:35: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/flat_array.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/ips4o.hpp:47: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/memory.hpp:50: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/buffers.hpp:65:55: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] 65 | static constexpr const bool kInitializedStorage = IS_TRIVIALLY_DEFAULT_CONSTRUCTIBLE(value_type); | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/buffers.hpp:45:47: note: expanded from macro 'IS_TRIVIALLY_DEFAULT_CONSTRUCTIBLE' 45 | #define IS_TRIVIALLY_DEFAULT_CONSTRUCTIBLE(T) __has_trivial_constructor(T) | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/buffers.hpp:139:52: note: in instantiation of static data member 'ips4o::detail::Sorter, std::greater>>::Block::kInitializedStorage' requested here 139 | using storage_type = typename std::conditional, std::greater>>::Block' requested here 230 | static_assert(sizeof(Block) == sizeof(typename Cfg::value_type) * Cfg::kBlockSize, "Block size mismatch."); | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/memory.hpp:174:13: note: in instantiation of member class 'ips4o::detail::Sorter, std::greater>>::Buffers' requested here 174 | Buffers buffers; | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/memory.hpp:76:31: note: in instantiation of member class 'ips4o::detail::Sorter, std::greater>>::LocalData' requested here 76 | : alloc_(new char[sizeof(T) + alignment]) | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/sequential.hpp:106:7: note: in instantiation of function template specialization 'ips4o::detail::AlignedPtr, std::greater>>::LocalData>::AlignedPtr, char *&>' requested here 106 | , local_ptr_(Cfg::kDataAlignment, std::move(comp), buffer_storage) {} | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/parallel.hpp:163:15: note: in instantiation of member function 'ips4o::SequentialSorter, std::greater>>::SequentialSorter' requested here 163 | , task_sorter_(false, {}, buffer_storage_.forThread(0)) | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/ips4o.hpp:106:12: note: in instantiation of member function 'ips4o::ParallelSorter::Iterator, Search::Hit::CmpQueryTarget>>::ParallelSorter' requested here 106 | return ParallelSorter>( | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/ips4o.hpp:130:26: note: in instantiation of function template specialization 'ips4o::parallel::make_sorter::Iterator, ips4o::Config<>, Search::Hit::CmpQueryTarget>' requested here 130 | ips4o::parallel::make_sorter(num_threads, std::move(comp)) | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/table.cpp:159:19: note: in instantiation of function template specialization 'ips4o::parallel::sort, Deque::Iterator, Search::Hit::CmpQueryTarget>' requested here 159 | ips4o::parallel::sort(hits.begin(), hits.end(), Search::Hit::CmpQueryTarget(), config.threads_); | ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/table.cpp:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/global_ranking.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../target.h:35: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/flat_array.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/ips4o.hpp:47: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/memory.hpp:50: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/buffers.hpp:231:19: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] 231 | static_assert(IS_TRIVIALLY_DEFAULT_CONSTRUCTIBLE(Block), "Block must be trivially default constructible."); | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/buffers.hpp:45:47: note: expanded from macro 'IS_TRIVIALLY_DEFAULT_CONSTRUCTIBLE' 45 | #define IS_TRIVIALLY_DEFAULT_CONSTRUCTIBLE(T) __has_trivial_constructor(T) | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/memory.hpp:174:13: note: in instantiation of member class 'ips4o::detail::Sorter, std::greater>>::Buffers' requested here 174 | Buffers buffers; | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/memory.hpp:76:31: note: in instantiation of member class 'ips4o::detail::Sorter, std::greater>>::LocalData' requested here 76 | : alloc_(new char[sizeof(T) + alignment]) | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/sequential.hpp:106:7: note: in instantiation of function template specialization 'ips4o::detail::AlignedPtr, std::greater>>::LocalData>::AlignedPtr, char *&>' requested here 106 | , local_ptr_(Cfg::kDataAlignment, std::move(comp), buffer_storage) {} | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/parallel.hpp:163:15: note: in instantiation of member function 'ips4o::SequentialSorter, std::greater>>::SequentialSorter' requested here 163 | , task_sorter_(false, {}, buffer_storage_.forThread(0)) | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/ips4o.hpp:106:12: note: in instantiation of member function 'ips4o::ParallelSorter::Iterator, Search::Hit::CmpQueryTarget>>::ParallelSorter' requested here 106 | return ParallelSorter>( | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/ips4o.hpp:130:26: note: in instantiation of function template specialization 'ips4o::parallel::make_sorter::Iterator, ips4o::Config<>, Search::Hit::CmpQueryTarget>' requested here 130 | ips4o::parallel::make_sorter(num_threads, std::move(comp)) | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/table.cpp:159:19: note: in instantiation of function template specialization 'ips4o::parallel::sort, Deque::Iterator, Search::Hit::CmpQueryTarget>' requested here 159 | ips4o::parallel::sort(hits.begin(), hits.end(), Search::Hit::CmpQueryTarget(), config.threads_); | ^ 10 warnings and 2 errors generated. [ 80% 158/194] /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/search/seed_complexity.cpp.o -MF CMakeFiles/diamond.dir/src/search/seed_complexity.cpp.o.d -o CMakeFiles/diamond.dir/src/search/seed_complexity.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/search/seed_complexity.cpp [ 81% 158/194] /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/tools/view.cpp.o -MF CMakeFiles/diamond.dir/src/tools/view.cpp.o.d -o CMakeFiles/diamond.dir/src/tools/view.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/tools/view.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/tools/view.cpp:9: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/tools/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] 148 | virtual OutputFormat* clone() const | ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/tools/../output/output_format.h:75:24: note: overridden virtual function is here 75 | virtual OutputFormat* clone() const = 0; | ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/tools/view.cpp:10: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/tools/../output/output.h:99:5: warning: field 'sep' will be initialized after field 'first' [-Wreorder-ctor] 99 | sep(sep), | ^~~~~~~~ | first(first) 100 | first(first) | ~~~~~~~~~~~~ | sep(sep) /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/tools/view.cpp:101:147: warning: missing field 'acc_stats' initializer [-Wmissing-field-initializers] 101 | Output::Info info{ SeqInfo { 0, 0, query_acc.c_str(), "", query_seq.source().length(), query_seq.source(), Sequence()}, false, nullptr, *out, {} }; | ^ 3 warnings generated. ninja: build stopped: subcommand failed. ===> 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 in /usr/ports/biology/diamond