[package - main-amd64-default][biology/diamond] Failed for diamond-2.1.8 in build
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Date: Sat, 16 Dec 2023 23:04:49 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: 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. !!!
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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
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SCRIPTPREFIX=/usr/local/share/poudriere
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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---
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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--
=======================<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
===> 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
===========================================================================
=======================<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 diamond-2.1.8 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 diamond-2.1.8 for building
=> SHA256 Checksum OK for bbuchfink-diamond-v2.1.8_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 diamond-2.1.8 for building
===> Extracting for diamond-2.1.8
=> SHA256 Checksum OK for bbuchfink-diamond-v2.1.8_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 diamond-2.1.8
===========================================================================
=======================<phase: build-depends >============================
===== 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
<snip>
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<std::_ClassicAlgPolicy, Search::Hit::CmpSubject &, Deque<Search::Hit, 28, Async>::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<std::_ClassicAlgPolicy, Deque<Search::Hit, 28, Async>::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<std::_ClassicAlgPolicy, Search::Hit::CmpSubject &, Deque<Search::Hit, 28, Async>::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<std::_ClassicAlgPolicy, Deque<Search::Hit, 28, Async>::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<std::_ClassicAlgPolicy, Deque<Search::Hit, 28, Async>::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<Deque<Search::Hit, 28, Async>::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<Deque<Search::Hit, 28, Async>::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<ips4o::ExtendedConfig<Deque<Search::Hit, 28, Async>::Iterator, Search::Hit::CmpQueryTarget>>::Block::kInitializedStorage' requested here
139 | using storage_type = typename std::conditional<kInitializedStorage, value_type,
| ^
/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/buffers.hpp:230:19: note: in instantiation of member class 'ips4o::detail::Sorter<ips4o::ExtendedConfig<Deque<Search::Hit, 28, Async>::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<ips4o::ExtendedConfig<Deque<Search::Hit, 28, Async>::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<ips4o::ExtendedConfig<Deque<Search::Hit, 28, Async>::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<ips4o::detail::Sorter<ips4o::ExtendedConfig<Deque<Search::Hit, 28, Async>::Iterator, Search::Hit::CmpQueryTarget>>::LocalData>::AlignedPtr<Search::Hit::CmpQueryTarget, char *>' 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<ips4o::ExtendedConfig<Deque<Search::Hit, 28, Async>::Iterator, Search::Hit::CmpQueryTarget>>::SequentialSorter' requested here
71 | ips4o::SequentialSorter<ips4o::ExtendedConfig<It, Comp, Cfg>> 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<ips4o::Config<>, Deque<Search::Hit, 28, Async>::Iterator, Search::Hit::CmpQueryTarget>' requested here
128 | ips4o::sort<Cfg>(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<ips4o::Config<>, Deque<Search::Hit, 28, Async>::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<ips4o::ExtendedConfig<Deque<Search::Hit, 28, Async>::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<ips4o::ExtendedConfig<Deque<Search::Hit, 28, Async>::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<ips4o::detail::Sorter<ips4o::ExtendedConfig<Deque<Search::Hit, 28, Async>::Iterator, Search::Hit::CmpQueryTarget>>::LocalData>::AlignedPtr<Search::Hit::CmpQueryTarget, char *>' 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<ips4o::ExtendedConfig<Deque<Search::Hit, 28, Async>::Iterator, Search::Hit::CmpQueryTarget>>::SequentialSorter' requested here
71 | ips4o::SequentialSorter<ips4o::ExtendedConfig<It, Comp, Cfg>> 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<ips4o::Config<>, Deque<Search::Hit, 28, Async>::Iterator, Search::Hit::CmpQueryTarget>' requested here
128 | ips4o::sort<Cfg>(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<ips4o::Config<>, Deque<Search::Hit, 28, Async>::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<ips4o::ExtendedConfig<std::__wrap_iter<ips4o::detail::ParallelTask *>, std::greater<ips4o::detail::ParallelTask>>>::Block::kInitializedStorage' requested here
139 | using storage_type = typename std::conditional<kInitializedStorage, value_type,
| ^
/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../util/data_structures/../../lib/ips4o/buffers.hpp:230:19: note: in instantiation of member class 'ips4o::detail::Sorter<ips4o::ExtendedConfig<std::__wrap_iter<ips4o::detail::ParallelTask *>, std::greater<ips4o::detail::ParallelTask>>>::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<ips4o::ExtendedConfig<std::__wrap_iter<ips4o::detail::ParallelTask *>, std::greater<ips4o::detail::ParallelTask>>>::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<ips4o::ExtendedConfig<std::__wrap_iter<ips4o::detail::ParallelTask *>, std::greater<ips4o::detail::ParallelTask>>>::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<ips4o::detail::Sorter<ips4o::ExtendedConfig<std::__wrap_iter<ips4o::detail::ParallelTask *>, std::greater<ips4o::detail::ParallelTask>>>::LocalData>::AlignedPtr<std::greater<ips4o::detail::ParallelTask>, 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<ips4o::ExtendedConfig<std::__wrap_iter<ips4o::detail::ParallelTask *>, std::greater<ips4o::detail::ParallelTask>>>::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<ips4o::ExtendedConfig<Deque<Search::Hit, 28, Async>::Iterator, Search::Hit::CmpQueryTarget>>::ParallelSorter' requested here
106 | return ParallelSorter<ExtendedConfig<It, Comp, Cfg>>(
| ^
/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<Deque<Search::Hit, 28, Async>::Iterator, ips4o::Config<>, Search::Hit::CmpQueryTarget>' requested here
130 | ips4o::parallel::make_sorter<It, Cfg>(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<ips4o::Config<>, Deque<Search::Hit, 28, Async>::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<ips4o::ExtendedConfig<std::__wrap_iter<ips4o::detail::ParallelTask *>, std::greater<ips4o::detail::ParallelTask>>>::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<ips4o::ExtendedConfig<std::__wrap_iter<ips4o::detail::ParallelTask *>, std::greater<ips4o::detail::ParallelTask>>>::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<ips4o::detail::Sorter<ips4o::ExtendedConfig<std::__wrap_iter<ips4o::detail::ParallelTask *>, std::greater<ips4o::detail::ParallelTask>>>::LocalData>::AlignedPtr<std::greater<ips4o::detail::ParallelTask>, 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<ips4o::ExtendedConfig<std::__wrap_iter<ips4o::detail::ParallelTask *>, std::greater<ips4o::detail::ParallelTask>>>::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<ips4o::ExtendedConfig<Deque<Search::Hit, 28, Async>::Iterator, Search::Hit::CmpQueryTarget>>::ParallelSorter' requested here
106 | return ParallelSorter<ExtendedConfig<It, Comp, Cfg>>(
| ^
/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<Deque<Search::Hit, 28, Async>::Iterator, ips4o::Config<>, Search::Hit::CmpQueryTarget>' requested here
130 | ips4o::parallel::make_sorter<It, Cfg>(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<ips4o::Config<>, Deque<Search::Hit, 28, Async>::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