From nobody Tue Dec 26 03:42:09 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 4SzgZB2KKFz55St2 for ; Tue, 26 Dec 2023 03:42:10 +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 4SzgZB01fRz4dsH for ; Tue, 26 Dec 2023 03:42:10 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1703562130; a=rsa-sha256; cv=none; b=MOGACBYTM1wU2OejMHdnY+DahZwPDOOaLGcRs1U0tOadsUcouepJOHHh5i4y4o4qh+YL/T r26poaQYs5yNMiN4/aSw+T++Ve9n3an4v/qRRaGzO7vZU7GzsoIP7Q+0VVzp9UM0w2y5IQ te1Pxl38/vZAUh075J1VGdYxSVa6viJWn17UG+M7Dpp78lEdIphvp7B0WsfyObVw81/EVt opagkXLNa8Mz6geIBIYCQRpgYjYkPTAe/iNOP3NMVdd/C3S5XYSy4PLeC2BANfqY51UYnh vsNcOsBqotUtG88j633Y8flqiBzrnvG5whwTP4gEVEnOe1ZIffZJEgHTTEGGCw== 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=1703562130; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=6XJbyCb4tMXw32DyjAIABLByooMxhcvKWj6u9NkI+RQ=; b=u9Wa6LniS5fgvlfyDkdKz7X1azUTEpiKRavDyQxmoJwJtpjH9egPRqptDvYR77zJg1sk7V 8N9/pkXL37kQMNDaeu8s8HXivxQzIdbB9K8rVe0XlROW3/zvBeJqqozAC1xduH0phSK+uq WcmxVxjP9BUQf2wOXv5bIVzqyejsEpoBm4EyEG9YMWbo/PrREIz5p1Cd/bEHr0NYlm72Yg LugQ0yRotR/o+ZKDSoIm+kveDyMRI3oV+4fc8YRDS4NEMvgYl8ApGxB9ZwwtDFVhrcdNQS /cKnHXRGuyYG2sEJTpgqIh8jqXvCC3LqvwdgqR3gr7JQqb/ppk2quZhqFiZsIg== Received: from foul2.nyi.freebsd.org (foul2.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:27]) (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 did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4SzgZ96Ch1zfLg for ; Tue, 26 Dec 2023 03:42:09 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from foul2.nyi.freebsd.org (localhost [127.0.0.1]) by foul2.nyi.freebsd.org (8.17.1/8.17.1) with ESMTP id 3BQ3g9Iv065473 for ; Tue, 26 Dec 2023 03:42:09 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by foul2.nyi.freebsd.org (8.17.1/8.17.1/Submit) id 3BQ3g9oD065471; Tue, 26 Dec 2023 03:42:09 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Tue, 26 Dec 2023 03:42:09 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202312260342.3BQ3g9oD065471@foul2.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 132powerpc64le-quarterly][biology/seqwish] Failed for seqwish-0.7.9 in build 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: 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 OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE UNAME_r=13.2-RELEASE 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/132powerpc64le-quarterly/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/132powerpc64le-quarterly/23/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=132powerpc64le-quarterly SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/132powerpc64le-quarterly/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--- ===> 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-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user =========================================================================== =================================================== ===== 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 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== 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 =========================================================================== =================================================== ===== 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. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== 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. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== 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 =========================================================================== =================================================== ===== 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 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ^~~~~~~~~~~~~~~ ::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)>::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 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::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 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); ^~~~~~~~~~~~~~~ ::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::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::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::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::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::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::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::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