[package - 132powerpc64le-quarterly][biology/seqwish] Failed for seqwish-0.7.9 in build
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Date: Tue, 26 Dec 2023 03:42:09 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/132powerpc64le-quarterly/74b68b434d29/logs/seqwish-0.7.9.log
Build URL: https://pkg-status.freebsd.org/foul2/build.html?mastername=132powerpc64le-quarterly&build=74b68b434d29
Log:
=>> Building biology/seqwish
build started at Tue Dec 26 03:37:05 UTC 2023
port directory: /usr/ports/biology/seqwish
package name: seqwish-0.7.9
building for: FreeBSD 132powerpc64le-quarterly-job-23 13.2-RELEASE FreeBSD 13.2-RELEASE powerpc
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 777 Oct 3 01:04 /usr/ports/biology/seqwish/Makefile
Ports top last git commit: 74b68b434
Ports top unclean checkout: no
Port dir last git commit: 2195304f9
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.0
Host OSVERSION: 1500000
Jail OSVERSION: 1302001
Job Id: 23
---Begin Environment---
SHELL=/bin/csh
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LC_COLLATE=C
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SAVED_TERM=
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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---
===> 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=13.2 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
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 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
[132powerpc64le-quarterly-job-23] Installing pkg-1.20.9...
[132powerpc64le-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-3.26.1_3.pkg
[132powerpc64le-quarterly-job-23] Installing cmake-core-3.26.1_3...
[132powerpc64le-quarterly-job-23] `-- Installing expat-2.5.0...
[132powerpc64le-quarterly-job-23] `-- Extracting expat-2.5.0: .......... done
[132powerpc64le-quarterly-job-23] `-- Installing jsoncpp-1.9.5...
[132powerpc64le-quarterly-job-23] `-- Extracting jsoncpp-1.9.5: .......... done
[132powerpc64le-quarterly-job-23] `-- Installing libuv-1.46.0...
[132powerpc64le-quarterly-job-23] `-- Extracting libuv-1.46.0: .......... done
[132powerpc64le-quarterly-job-23] `-- Installing rhash-1.4.4...
[132powerpc64le-quarterly-job-23] | `-- Installing gettext-runtime-0.22_1...
[132powerpc64le-quarterly-job-23] | | `-- Installing indexinfo-0.3.1...
[132powerpc64le-quarterly-job-23] | | `-- Extracting indexinfo-0.3.1: .... done
[132powerpc64le-quarterly-job-23] | `-- Extracting gettext-runtime-0.22_1: .......... done
[132powerpc64le-quarterly-job-23] `-- Extracting rhash-1.4.4: .......... done
[132powerpc64le-quarterly-job-23] Extracting cmake-core-3.26.1_3: .......... 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<'\x00'>, sdsl::isa_sampling<'\x00'>, 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<'\x00'>, sdsl::isa_sampling<'\x00'>, 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<'\x00'>, sdsl::isa_sampling<'\x00'>, 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