[package - 140releng-powerpc64le-quarterly][biology/seqwish] Failed for seqwish-0.7.9 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Thu, 15 Feb 2024 21:37:51 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.

Maintainer:     yuri@FreeBSD.org
Log URL:        https://pkg-status.freebsd.org/foul2/data/140releng-powerpc64le-quarterly/b3e5282399eb/logs/seqwish-0.7.9.log
Build URL:      https://pkg-status.freebsd.org/foul2/build.html?mastername=140releng-powerpc64le-quarterly&build=b3e5282399eb
Log:

=>> Building biology/seqwish
build started at Thu Feb 15 21:32:13 UTC 2024
port directory: /usr/ports/biology/seqwish
package name: seqwish-0.7.9
building for: FreeBSD 140releng-powerpc64le-quarterly-job-23 14.0-RC3 FreeBSD 14.0-RC3 1400097 powerpc
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r--  1 root wheel 839 Jan  6 01:03 /usr/ports/biology/seqwish/Makefile
Ports top last git commit: b3e528239
Ports top unclean checkout: no
Port dir last git commit: 756e18783
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1
Host OSVERSION: 1500000
Jail OSVERSION: 1400097
Job Id: 23

---Begin Environment---
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LC_COLLATE=C
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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---
===> The following configuration options are available for seqwish-0.7.9:
     OPENMP=on: Parallel processing support via OpenMP
===> Use 'make config' to modify these settings
---End OPTIONS List---

--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqwish/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqwish/work  XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqwish/work/.cache  HOME=/wrkdirs/usr/ports/biology/seqwish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqwish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqwish/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--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqwish/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqwish/work  XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqwish/work/.cache  HOME=/wrkdirs/usr/ports/biology/seqwish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqwish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqwish/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="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  -fopenmp "  MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install  -s -m 555"  BSD_INSTALL_LIB="install  -s -m 0644"  BSD_INSTALL_SCRIPT="install  -m 555"  BSD_INSTALL_D
 ATA="install  -m 0644"  BSD_INSTALL_MAN="install  -m 444"
--End MAKE_ENV--

--PLIST_SUB--
 CMAKE_BUILD_TYPE="release" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/seqwish"  EXAMPLESDIR="share/examples/seqwish"  DATADIR="share/seqwish"  WWWDIR="www/seqwish"  ETCDIR="etc/seqwish"
--End PLIST_SUB--

--SUB_LIST--
 PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/seqwish DOCSDIR=/usr/local/share/doc/seqwish EXAMPLESDIR=/usr/local/share/examples/seqwish  WWWDIR=/usr/local/www/seqwish ETCDIR=/usr/local/etc/seqwish
--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
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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 MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   seqwish-0.7.9 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.20.9.pkg
[140releng-powerpc64le-quarterly-job-23] Installing pkg-1.20.9...
[140releng-powerpc64le-quarterly-job-23] Extracting pkg-1.20.9: .......... done
===>   seqwish-0.7.9 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of seqwish-0.7.9
===========================================================================
=======================<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 MIT accepted by the user
===> Fetching all distfiles required by seqwish-0.7.9 for building
===========================================================================
=======================<phase: checksum       >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  License MIT accepted by the user
===> Fetching all distfiles required by seqwish-0.7.9 for building
=> SHA256 Checksum OK for seqwish-v0.7.9.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 MIT accepted by the user
===> Fetching all distfiles required by seqwish-0.7.9 for building
===>  Extracting for seqwish-0.7.9
=> SHA256 Checksum OK for seqwish-v0.7.9.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 seqwish-0.7.9
===>  Applying FreeBSD patches for seqwish-0.7.9 from /usr/ports/biology/seqwish/files
===========================================================================
=======================<phase: build-depends  >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   seqwish-0.7.9 depends on file: /usr/local/bin/cmake - not found
===>   Installing existing package /packages/All/cmake-core-3.28.1.pkg
[140releng-powerpc64le-quarterly-job-23] Installing cmake-core-3.28.1...
[140releng-powerpc64le-quarterly-job-23] `-- Installing expat-2.5.0...
[140releng-powerpc64le-quarterly-job-23] `-- Extracting expat-2.5.0: .......... done
[140releng-powerpc64le-quarterly-job-23] `-- Installing jsoncpp-1.9.5...
[140releng-powerpc64le-quarterly-job-23] `-- Extracting jsoncpp-1.9.5: .......... done
[140releng-powerpc64le-quarterly-job-23] `-- Installing libuv-1.47.0...
[140releng-powerpc64le-quarterly-job-23] `-- Extracting libuv-1.47.0: .......... done
[140releng-powerpc64le-quarterly-job-23] `-- Installing rhash-1.4.4...
[140releng-powerpc64le-quarterly-job-23] |   `-- Installing gettext-runtime-0.22.3...
[140releng-powerpc64le-quarterly-job-23] |   | `-- Installing indexinfo-0.3.1...
[140releng-powerpc64le-quarterly-job-23] |   | `-- Extracting indexinfo-0.3.1: .... done
[140releng-powerpc64le-quarterly-job-23] |   `-- Extracting gettext-runtime-0.22.3: .......... done
[140releng-powerpc64le-quarterly-job-23] `-- Extracting rhash-1.4.4: .......... done
[140releng-powerpc64le-quarterly-job-23] Extracting cmake-core-3.28.1: .......... done
===>   seqwish-0.7.9 depends on file: /usr/local/bin/cmake - found
===>   Returning to build of seqwish-0.7.9
===========================================================================
=======================<phase: lib-depends    >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: configure      >============================
<snip>
                    ^~~~~~~~~~~~~~~
                    ::atomic_queue::spin_loop_pause
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:41:20: note: '::atomic_queue::spin_loop_pause' declared here
static inline void spin_loop_pause() noexcept {
                   ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:242:21: error: use of undeclared identifier 'spin_loop_pause'; did you mean '::atomic_queue::spin_loop_pause'?
                    spin_loop_pause();
                    ^~~~~~~~~~~~~~~
                    ::atomic_queue::spin_loop_pause
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:41:20: note: '::atomic_queue::spin_loop_pause' declared here
static inline void spin_loop_pause() noexcept {
                   ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:254:21: error: use of undeclared identifier 'spin_loop_pause'; did you mean '::atomic_queue::spin_loop_pause'?
                    spin_loop_pause();
                    ^~~~~~~~~~~~~~~
                    ::atomic_queue::spin_loop_pause
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:41:20: note: '::atomic_queue::spin_loop_pause' declared here
static inline void spin_loop_pause() noexcept {
                   ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:260:21: error: use of undeclared identifier 'spin_loop_pause'; did you mean '::atomic_queue::spin_loop_pause'?
                    spin_loop_pause(); // (1) Wait for store (2) to complete.
                    ^~~~~~~~~~~~~~~
                    ::atomic_queue::spin_loop_pause
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:41:20: note: '::atomic_queue::spin_loop_pause' declared here
static inline void spin_loop_pause() noexcept {
                   ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:273:21: error: use of undeclared identifier 'spin_loop_pause'; did you mean '::atomic_queue::spin_loop_pause'?
                    spin_loop_pause();
                    ^~~~~~~~~~~~~~~
                    ::atomic_queue::spin_loop_pause
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:41:20: note: '::atomic_queue::spin_loop_pause' declared here
static inline void spin_loop_pause() noexcept {
                   ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:288:21: error: use of undeclared identifier 'spin_loop_pause'; did you mean '::atomic_queue::spin_loop_pause'?
                    spin_loop_pause();
                    ^~~~~~~~~~~~~~~
                    ::atomic_queue::spin_loop_pause
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:41:20: note: '::atomic_queue::spin_loop_pause' declared here
static inline void spin_loop_pause() noexcept {
                   ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:299:21: error: use of undeclared identifier 'spin_loop_pause'; did you mean '::atomic_queue::spin_loop_pause'?
                    spin_loop_pause();
                    ^~~~~~~~~~~~~~~
                    ::atomic_queue::spin_loop_pause
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:41:20: note: '::atomic_queue::spin_loop_pause' declared here
static inline void spin_loop_pause() noexcept {
                   ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:313:21: error: use of undeclared identifier 'spin_loop_pause'; did you mean '::atomic_queue::spin_loop_pause'?
                    spin_loop_pause();
                    ^~~~~~~~~~~~~~~
                    ::atomic_queue::spin_loop_pause
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:41:20: note: '::atomic_queue::spin_loop_pause' declared here
static inline void spin_loop_pause() noexcept {
                   ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:406:98: error: use of undeclared identifier 'CACHE_LINE_SIZE'; did you mean '::atomic_queue::CACHE_LINE_SIZE'?
    static constexpr int SHUFFLE_BITS = details::GetIndexShuffleBits<MINIMIZE_CONTENTION, size_, CACHE_LINE_SIZE / sizeof(std::atomic<T>)>::value;
                                                                                                 ^~~~~~~~~~~~~~~
                                                                                                 ::atomic_queue::CACHE_LINE_SIZE
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:40:15: note: '::atomic_queue::CACHE_LINE_SIZE' declared here
constexpr int CACHE_LINE_SIZE = 128; // TODO: Review that this is the correct value.
              ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:411:13: error: use of undeclared identifier 'CACHE_LINE_SIZE'; did you mean '::atomic_queue::CACHE_LINE_SIZE'?
    alignas(CACHE_LINE_SIZE) std::atomic<T> elements_[size_] = {}; // Empty elements are NIL.
            ^~~~~~~~~~~~~~~
            ::atomic_queue::CACHE_LINE_SIZE
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:40:15: note: '::atomic_queue::CACHE_LINE_SIZE' declared here
constexpr int CACHE_LINE_SIZE = 128; // TODO: Review that this is the correct value.
              ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:446:98: error: use of undeclared identifier 'CACHE_LINE_SIZE'; did you mean '::atomic_queue::CACHE_LINE_SIZE'?
    static constexpr int SHUFFLE_BITS = details::GetIndexShuffleBits<MINIMIZE_CONTENTION, size_, CACHE_LINE_SIZE / sizeof(State)>::value;
                                                                                                 ^~~~~~~~~~~~~~~
                                                                                                 ::atomic_queue::CACHE_LINE_SIZE
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:40:15: note: '::atomic_queue::CACHE_LINE_SIZE' declared here
constexpr int CACHE_LINE_SIZE = 128; // TODO: Review that this is the correct value.
              ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:451:13: error: use of undeclared identifier 'CACHE_LINE_SIZE'; did you mean '::atomic_queue::CACHE_LINE_SIZE'?
    alignas(CACHE_LINE_SIZE) std::atomic<unsigned char> states_[size_] = {};
            ^~~~~~~~~~~~~~~
            ::atomic_queue::CACHE_LINE_SIZE
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:40:15: note: '::atomic_queue::CACHE_LINE_SIZE' declared here
constexpr int CACHE_LINE_SIZE = 128; // TODO: Review that this is the correct value.
              ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:452:13: error: use of undeclared identifier 'CACHE_LINE_SIZE'; did you mean '::atomic_queue::CACHE_LINE_SIZE'?
    alignas(CACHE_LINE_SIZE) T elements_[size_] = {};
            ^~~~~~~~~~~~~~~
            ::atomic_queue::CACHE_LINE_SIZE
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:40:15: note: '::atomic_queue::CACHE_LINE_SIZE' declared here
constexpr int CACHE_LINE_SIZE = 128; // TODO: Review that this is the correct value.
              ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:487:53: error: use of undeclared identifier 'CACHE_LINE_SIZE'; did you mean '::atomic_queue::CACHE_LINE_SIZE'?
    static constexpr auto ELEMENTS_PER_CACHE_LINE = CACHE_LINE_SIZE / sizeof(std::atomic<T>);
                                                    ^~~~~~~~~~~~~~~
                                                    ::atomic_queue::CACHE_LINE_SIZE
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:40:15: note: '::atomic_queue::CACHE_LINE_SIZE' declared here
constexpr int CACHE_LINE_SIZE = 128; // TODO: Review that this is the correct value.
              ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:495:13: error: use of undeclared identifier 'CACHE_LINE_SIZE'; did you mean '::atomic_queue::CACHE_LINE_SIZE'?
    alignas(CACHE_LINE_SIZE) unsigned size_;
            ^~~~~~~~~~~~~~~
            ::atomic_queue::CACHE_LINE_SIZE
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:40:15: note: '::atomic_queue::CACHE_LINE_SIZE' declared here
constexpr int CACHE_LINE_SIZE = 128; // TODO: Review that this is the correct value.
              ^
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/main.cpp:14:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/transclosure.hpp:22:
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/paryfor/paryfor.hpp:572:13: error: use of undeclared identifier 'CACHE_LINE_SIZE'; did you mean '::atomic_queue::CACHE_LINE_SIZE'?
    alignas(CACHE_LINE_SIZE) unsigned size_;
            ^~~~~~~~~~~~~~~
            ::atomic_queue::CACHE_LINE_SIZE
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue/defs.h:40:15: note: '::atomic_queue::CACHE_LINE_SIZE' declared here
constexpr int CACHE_LINE_SIZE = 128; // TODO: Review that this is the correct value.
              ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
*** [CMakeFiles/seqwish.dir/src/main.cpp.o] Error code 1

make[3]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build
--- CMakeFiles/seqwish.dir/src/seqindex.cpp.o ---
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/seqindex.cpp:1:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/seqindex.hpp:11:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/csa_wt.hpp:24:
In file included from /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/wavelet_trees.hpp:41:
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/construct.hpp:124:79: warning: instantiation of variable 'sdsl::key_text_trait<'\b'>::KEY_TEXT' required here, but no definition is available [-Wundefined-var-template]
    const char* KEY_TEXT = key_text_trait<t_index::alphabet_category::WIDTH>::KEY_TEXT;
                                                                              ^
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/construct.hpp:90:5: note: in instantiation of function template specialization 'sdsl::construct<sdsl::csa_wt<sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<'\x01'>, sdsl::rank_support_v<'\x01', '\x01'>, sdsl::select_support_mcl<'\x01', '\x01'>, sdsl::select_support_mcl<'\x00', '\x01'>>, 32, 64, sdsl::sa_order_sa_sampling<>, sdsl::isa_sampling<>, sdsl::byte_alphabet>>' requested here
    construct(idx, file, config, num_bytes, index_tag);
    ^
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/construct.hpp:63:5: note: in instantiation of function template specialization 'sdsl::construct<sdsl::csa_wt<sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<'\x01'>, sdsl::rank_support_v<'\x01', '\x01'>, sdsl::select_support_mcl<'\x01', '\x01'>, sdsl::select_support_mcl<'\x00', '\x01'>>, 32, 64, sdsl::sa_order_sa_sampling<>, sdsl::isa_sampling<>, sdsl::byte_alphabet>>' requested here
    construct(idx, file, config, num_bytes);
    ^
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/src/seqindex.cpp:91:5: note: in instantiation of function template specialization 'sdsl::construct<sdsl::csa_wt<sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<'\x01'>, sdsl::rank_support_v<'\x01', '\x01'>, sdsl::select_support_mcl<'\x01', '\x01'>, sdsl::select_support_mcl<'\x00', '\x01'>>, 32, 64, sdsl::sa_order_sa_sampling<>, sdsl::isa_sampling<>, sdsl::byte_alphabet>>' requested here
    construct(seq_name_csa, seqnamefile, 1);
    ^
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/config.hpp:51:24: note: forward declaration of template entity is here
    static const char* KEY_TEXT;
                       ^
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/construct.hpp:124:79: note: add an explicit instantiation declaration to suppress this warning if 'sdsl::key_text_trait<'\b'>::KEY_TEXT' is explicitly instantiated in another translation unit
    const char* KEY_TEXT = key_text_trait<t_index::alphabet_category::WIDTH>::KEY_TEXT;
                                                                              ^
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/construct.hpp:125:78: warning: instantiation of variable 'sdsl::key_bwt_trait<'\b'>::KEY_BWT' required here, but no definition is available [-Wundefined-var-template]
    const char* KEY_BWT  = key_bwt_trait<t_index::alphabet_category::WIDTH>::KEY_BWT;
                                                                             ^
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/config.hpp:57:24: note: forward declaration of template entity is here
    static const char* KEY_BWT;
                       ^
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/construct.hpp:125:78: note: add an explicit instantiation declaration to suppress this warning if 'sdsl::key_bwt_trait<'\b'>::KEY_BWT' is explicitly instantiated in another translation unit
    const char* KEY_BWT  = key_bwt_trait<t_index::alphabet_category::WIDTH>::KEY_BWT;
                                                                             ^
2 warnings generated.
1 error

make[3]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build
*** [CMakeFiles/seqwish.dir/all] Error code 2

make[2]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build
1 error

make[2]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build
*** [all] Error code 2

make[1]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build
1 error

make[1]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build
===> 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/seqwish