From owner-freebsd-pkg-fallout@freebsd.org Wed Jun 17 18:43:11 2020 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id C55D1357F60 for ; Wed, 17 Jun 2020 18:43:11 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (unknown [127.0.1.3]) by mx1.freebsd.org (Postfix) with ESMTP id 49nDTq58b8z4K4J for ; Wed, 17 Jun 2020 18:43:11 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id AF03E357BDC; Wed, 17 Jun 2020 18:43:11 +0000 (UTC) Delivered-To: pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id AD1A6357BDB for ; Wed, 17 Jun 2020 18:43:11 +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 "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 49nDTq4PXsz4KLS for ; Wed, 17 Jun 2020 18:43:11 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from thunderx1.nyi.freebsd.org (thunderx1.nyi.freebsd.org [IPv6:2610:1c1:1:6082::16:fb]) (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 91DD624B37 for ; Wed, 17 Jun 2020 18:43:11 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from thunderx1.nyi.freebsd.org (localhost [127.0.0.1]) by thunderx1.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id 05HIhBCR067690 for ; Wed, 17 Jun 2020 18:43:11 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by thunderx1.nyi.freebsd.org (8.15.2/8.15.2/Submit) id 05HIhB4x067686; Wed, 17 Jun 2020 18:43:11 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Wed, 17 Jun 2020 18:43:11 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202006171843.05HIhB4x067686@thunderx1.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 121arm64-quarterly][biology/hhsuite] Failed for hhsuite-3.2.0_3 in build X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.33 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 17 Jun 2020 18:43:11 -0000 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 Last committer: jbeich@FreeBSD.org Ident: $FreeBSD: branches/2020Q2/biology/hhsuite/Makefile 528082 2020-03-08 21:56:36Z jbeich $ Log URL: http://thunderx1.nyi.freebsd.org/data/121arm64-quarterly/538418/logs/hhsuite-3.2.0_3.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=121arm64-quarterly&build=538418 Log: =>> Building biology/hhsuite build started at Wed Jun 17 18:41:28 UTC 2020 port directory: /usr/ports/biology/hhsuite package name: hhsuite-3.2.0_3 building for: FreeBSD 121arm64-quarterly-job-07 12.1-RELEASE-p6 FreeBSD 12.1-RELEASE-p6 1201000 arm64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: branches/2020Q2/biology/hhsuite/Makefile 528082 2020-03-08 21:56:36Z jbeich $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300089 Jail OSVERSION: 1201000 Job Id: 07 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1201000 UNAME_v=FreeBSD 12.1-RELEASE-p6 1201000 UNAME_r=12.1-RELEASE-p6 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/121arm64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/121arm64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=121arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/121arm64-quarterly/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hhsuite/work HOME=/wrkdirs/usr/ports/biology/hhsuite/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hhsuite/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hhsuite/work HOME=/wrkdirs/usr/ports/biology/hhsuite/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hhsuite/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/hhsuite/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -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_INSTALL_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" PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=freebsd12 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=12.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.30.3 PERL_VER=5.30 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.30 DOCSDIR="share/doc/hhsuite" EXAMPLESDIR="share/examples/hhsuite" DATADIR="share/hhsuite" WWWDIR="www/hhsuite" ETCDIR="etc/hhsuite" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/hhsuite DOCSDIR=/usr/local/share/doc/hhsuite EXAMPLESDIR=/usr/local/share/examples/hhsuite WWWDIR=/usr/local/www/hhsuite ETCDIR=/usr/local/etc/hhsuite --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 #### /usr/local/etc/poudriere.d/make.conf #### # 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 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=12.1-RELEASE-p6 OSREL=12.1 OSVERSION=1201000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 1048576 stack size (kbytes, -s) 1048576 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) 1024 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-- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> hhsuite-3.2.0_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.13.2.txz [121arm64-quarterly-job-07] Installing pkg-1.13.2... [121arm64-quarterly-job-07] Extracting pkg-1.13.2: .......... done ===> hhsuite-3.2.0_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hhsuite-3.2.0_3 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hhsuite-3.2.0_3 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hhsuite-3.2.0_3 for building => SHA256 Checksum OK for soedinglab-hh-suite-v3.2.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hhsuite-3.2.0_3 for building ===> Extracting for hhsuite-3.2.0_3 => SHA256 Checksum OK for soedinglab-hh-suite-v3.2.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for hhsuite-3.2.0_3 ===> Applying FreeBSD patches for hhsuite-3.2.0_3 =========================================================================== =================================================== ===> hhsuite-3.2.0_3 depends on package: openmpi>0 - not found ===> Installing existing package /packages/All/openmpi-1.10.7_7.txz [121arm64-quarterly-job-07] Installing openmpi-1.10.7_7... [121arm64-quarterly-job-07] `-- Installing gcc9-9.3.0... [121arm64-quarterly-job-07] | `-- Installing binutils-2.33.1_2,1... [121arm64-quarterly-job-07] | | `-- Installing gettext-runtime-0.20.1... [121arm64-quarterly-job-07] | | `-- Installing indexinfo-0.3.1... [121arm64-quarterly-job-07] | | `-- Extracting indexinfo-0.3.1: .... done [121arm64-quarterly-job-07] | | `-- Extracting gettext-runtime-0.20.1: .......... done [121arm64-quarterly-job-07] | `-- Extracting binutils-2.33.1_2,1: .......... done [121arm64-quarterly-job-07] | `-- Installing gmp-6.2.0... [121arm64-quarterly-job-07] | `-- Extracting gmp-6.2.0: .......... done [121arm64-quarterly-job-07] | `-- Installing mpc-1.1.0_2... [121arm64-quarterly-job-07] | | `-- Installing mpfr-4.0.2... [121arm64-quarterly-job-07] | | `-- Extracting mpfr-4.0.2: .......... done [121arm64-quarterly-job-07] | `-- Extracting mpc-1.1.0_2: ......... done [121arm64-quarterly-job-07] `-- Extracting gcc9-9.3.0: .......... done [121arm64-quarterly-job-07] `-- Installing hwloc-1.11.11... [121arm64-quarterly-job-07] | `-- Installing libpciaccess-0.16... [121arm64-quarterly-job-07] | | `-- Installing pciids-20200324... [121arm64-quarterly-job-07] | | `-- Extracting pciids-20200324: ..... done -- Performing Test HAVE_SSE_EXTENSIONS - Failed -- SIMD: This platform doesn't have a supported SIMD instruction set, expect it to be slow. -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_COLOR_MAKEFILE CMAKE_C_FLAGS_DEBUG CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE Python_ADDITIONAL_VERSIONS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/hhsuite/work/.build =========================================================================== =================================================== ===> Building for hhsuite-3.2.0_3 [1/106] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ffindex_unpack.c [2/106] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong 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-I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ffindex_modify.c [5/106] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ffindex_reduce.c [6/106] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ffindex_from_fasta.c [7/106] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ffindex_from_fasta_with_split.c [8/106] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ffindex_build.c [9/106] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ffindex_apply_mpi.c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ffindex_apply_mpi.c:172:106: warning: format specifies type 'long long' but the argument has type 'long' [-Wformat] fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); ~~~~ ^~~~~~~~~~~ %ld 1 warning generated. [10/106] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ext -I/usr/local/mpi/openmpi/include -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_MPI=1 -pthread -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ffindex_apply_mpi.c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ffindex_apply_mpi.c:172:106: warning: format specifies type 'long long' but the argument has type 'long' [-Wformat] fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); ~~~~ ^~~~~~~~~~~ %ld 1 warning generated. [11/106] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ffutil.c [12/106] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ext -I/usr/local/mpi/openmpi/include -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath=-Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath -Wl,/usr/local/mpi/openmpi/lib -Wl,--enable-new-dtags -pthread -MD -MT lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o -MF lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o.d -o lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/mpq/mpq.c cc: warning: -Wl,-rpath=-Wl,-rpath=/usr/local/lib/gcc9: 'linker' input unused [-Wunused-command-line-argument] cc: warning: -Wl,-rpath: 'linker' input unused [-Wunused-command-line-argument] cc: warning: -Wl,/usr/local/mpi/openmpi/lib: 'linker' input unused [-Wunused-command-line-argument] cc: warning: -Wl,--enable-new-dtags: 'linker' input unused [-Wunused-command-line-argument] [13/106] : && /usr/local/bin/cmake -E remove lib/ffindex/src/mpq/libmpq.a && /usr/bin/ar qc lib/ffindex/src/mpq/libmpq.a lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o && /usr/bin/ranlib lib/ffindex/src/mpq/libmpq.a && : [14/106] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src/ffindex.c [15/106] : && /usr/local/bin/cmake -E remove lib/ffindex/src/libffindex.a && /usr/bin/ar qc lib/ffindex/src/libffindex.a lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o && /usr/bin/ranlib lib/ffindex/src/libffindex.a && : [16/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o lib/ffindex/src/ffindex_order lib/ffindex/src/libffindex.a && : [17/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o lib/ffindex/src/ffindex_unpack lib/ffindex/src/libffindex.a && : [18/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o lib/ffindex/src/ffindex_modify lib/ffindex/src/libffindex.a && : [19/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o lib/ffindex/src/ffindex_get lib/ffindex/src/libffindex.a && : [20/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o lib/ffindex/src/ffindex_reduce lib/ffindex/src/libffindex.a && : [21/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o lib/ffindex/src/ffindex_from_fasta lib/ffindex/src/libffindex.a && : [22/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o lib/ffindex/src/ffindex_from_fasta_with_split lib/ffindex/src/libffindex.a && : [23/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o lib/ffindex/src/ffindex_build lib/ffindex/src/libffindex.a && : [24/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong -Wl,-rpath=-Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath -Wl,/usr/local/mpi/openmpi/lib -Wl,--enable-new-dtags -pthread lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o -o lib/ffindex/src/ffindex_apply_mpi -Wl,-rpath,/usr/local/mpi/openmpi/lib: lib/ffindex/src/libffindex.a lib/ffindex/src/mpq/libmpq.a /usr/local/mpi/openmpi/lib/libmpi.so && : [25/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o lib/ffindex/src/ffindex_apply lib/ffindex/src/libffindex.a && : [26/106] cd /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/data && mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated && /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/cmake/xxdi.pl context_data.lib > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h.tmp /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h [27/106] cd /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/data && mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated && /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/cmake/xxdi.pl cs219.lib > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h.tmp /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h [28/106] cd /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/data && mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated && /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/cmake/xxdi.pl context_data.crf > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h.tmp && mv -f /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h.tmp /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h [29/106] /usr/bin/c++ -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -Isrc -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/a3m_compress.cpp [30/106] : && /usr/local/bin/cmake -E remove src/libA3M_COMPRESS.a && /usr/bin/ar qc src/libA3M_COMPRESS.a src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o && /usr/bin/ranlib src/libA3M_COMPRESS.a && : [31/106] /usr/bin/c++ -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -Isrc -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o -MF src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o.d -o src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhblits_app.cpp FAILED: src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o /usr/bin/c++ -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -Isrc -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o -MF src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o.d -o src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhblits_app.cpp In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhblits_app.cpp:1: In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhsearch.h:34: In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhblits.h:42: In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhdecl.h:18: /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:46:56: error: use of undeclared identifier 'ALIGN_FLOAT' size_t size_pointer_array = ICEIL(dim1*sizeof(T*), ALIGN_FLOAT); ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:46:56: error: use of undeclared identifier 'ALIGN_FLOAT' /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:46:56: error: use of undeclared identifier 'ALIGN_FLOAT' /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:47:48: error: use of undeclared identifier 'ALIGN_FLOAT' size_t dim2_padded = ICEIL(dim2*sizeof(T), ALIGN_FLOAT)/sizeof(T); ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:47:48: error: use of undeclared identifier 'ALIGN_FLOAT' /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:47:48: error: use of undeclared identifier 'ALIGN_FLOAT' /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:49:35: error: use of undeclared identifier 'ALIGN_FLOAT' T** matrix = (T**) mem_align( ALIGN_FLOAT, size_pointer_array + dim1*dim2_padded*sizeof(T) ); ^ In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhblits_app.cpp:1: In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhsearch.h:34: In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhblits.h:46: In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil.h:14: /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:371:8: error: unknown type name 'simd_float' inline simd_float simdf32_fpow2(simd_float X) { ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:371:33: error: unknown type name 'simd_float' inline simd_float simdf32_fpow2(simd_float X) { ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:373:5: error: unknown type name 'simd_int' simd_int* xPtr = (simd_int*) &X; // store address of float as pointer to int ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:373:23: error: use of undeclared identifier 'simd_int' simd_int* xPtr = (simd_int*) &X; // store address of float as pointer to int ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:373:32: error: expected expression simd_int* xPtr = (simd_int*) &X; // store address of float as pointer to int ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:375:11: error: unknown type name 'simd_float' const simd_float CONST32_05f = simdf32_set(0.5f); // Initialize a vector (4x32) with 0.5f ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:375:42: error: use of undeclared identifier 'simdf32_set' const simd_float CONST32_05f = simdf32_set(0.5f); // Initialize a vector (4x32) with 0.5f ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:377:11: error: unknown type name 'simd_int' const simd_int CONST32_3i = simdi32_set(3); ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:377:42: error: use of undeclared identifier 'simdi32_set' const simd_int CONST32_3i = simdi32_set(3); ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:378:11: error: unknown type name 'simd_int' const simd_int CONST32_3shift22 = simdi32_slli(CONST32_3i, 22); ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:379:11: error: unknown type name 'simd_float' const simd_float CONST32_1f = simdf32_set(1.0f); ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:379:42: error: use of undeclared identifier 'simdf32_set' const simd_float CONST32_1f = simdf32_set(1.0f); ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. [32/106] /usr/bin/c++ -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -Isrc -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_mpi.dir/hhblits_mpi.cpp.o -MF src/CMakeFiles/hhalign_mpi.dir/hhblits_mpi.cpp.o.d -o src/CMakeFiles/hhalign_mpi.dir/hhblits_mpi.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhblits_mpi.cpp FAILED: src/CMakeFiles/hhalign_mpi.dir/hhblits_mpi.cpp.o /usr/bin/c++ -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/lib/ffindex/src -Isrc -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_mpi.dir/hhblits_mpi.cpp.o -MF src/CMakeFiles/hhalign_mpi.dir/hhblits_mpi.cpp.o.d -o src/CMakeFiles/hhalign_mpi.dir/hhblits_mpi.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhblits_mpi.cpp In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhblits_mpi.cpp:8: In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhsearch.h:34: In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhblits.h:42: In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhdecl.h:18: /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:46:56: error: use of undeclared identifier 'ALIGN_FLOAT' size_t size_pointer_array = ICEIL(dim1*sizeof(T*), ALIGN_FLOAT); ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:46:56: error: use of undeclared identifier 'ALIGN_FLOAT' /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:46:56: error: use of undeclared identifier 'ALIGN_FLOAT' /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:47:48: error: use of undeclared identifier 'ALIGN_FLOAT' size_t dim2_padded = ICEIL(dim2*sizeof(T), ALIGN_FLOAT)/sizeof(T); ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:47:48: error: use of undeclared identifier 'ALIGN_FLOAT' /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:47:48: error: use of undeclared identifier 'ALIGN_FLOAT' /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/util.h:49:35: error: use of undeclared identifier 'ALIGN_FLOAT' T** matrix = (T**) mem_align( ALIGN_FLOAT, size_pointer_array + dim1*dim2_padded*sizeof(T) ); ^ In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhblits_mpi.cpp:8: In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhsearch.h:34: In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhblits.h:46: In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil.h:14: /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:371:8: error: unknown type name 'simd_float' inline simd_float simdf32_fpow2(simd_float X) { ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:371:33: error: unknown type name 'simd_float' inline simd_float simdf32_fpow2(simd_float X) { ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:373:5: error: unknown type name 'simd_int' simd_int* xPtr = (simd_int*) &X; // store address of float as pointer to int ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:373:23: error: use of undeclared identifier 'simd_int' simd_int* xPtr = (simd_int*) &X; // store address of float as pointer to int ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:373:32: error: expected expression simd_int* xPtr = (simd_int*) &X; // store address of float as pointer to int ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:375:11: error: unknown type name 'simd_float' const simd_float CONST32_05f = simdf32_set(0.5f); // Initialize a vector (4x32) with 0.5f ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:375:42: error: use of undeclared identifier 'simdf32_set' const simd_float CONST32_05f = simdf32_set(0.5f); // Initialize a vector (4x32) with 0.5f ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:377:11: error: unknown type name 'simd_int' const simd_int CONST32_3i = simdi32_set(3); ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:377:42: error: use of undeclared identifier 'simdi32_set' const simd_int CONST32_3i = simdi32_set(3); ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:378:11: error: unknown type name 'simd_int' const simd_int CONST32_3shift22 = simdi32_slli(CONST32_3i, 22); ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:379:11: error: unknown type name 'simd_float' const simd_float CONST32_1f = simdf32_set(1.0f); ^ /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.2.0/src/hhutil-inl.h:379:42: error: use of undeclared identifier 'simdf32_set' const simd_float CONST32_1f = simdf32_set(1.0f); ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors 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/hhsuite