From owner-freebsd-pkg-fallout@freebsd.org Tue Aug 6 02:29:17 2019 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 867EDB3940 for ; Tue, 6 Aug 2019 02:29:17 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (mailman.nyi.freebsd.org [IPv6:2610:1c1:1:606c::50:13]) by mx1.freebsd.org (Postfix) with ESMTP id 462dqx3phRz4Vwb for ; Tue, 6 Aug 2019 02:29:17 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id 82B87B393F; Tue, 6 Aug 2019 02:29:17 +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 8270EB393E for ; Tue, 6 Aug 2019 02:29:17 +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) server-signature RSA-PSS (4096 bits) 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 462dqx3frRz4VwZ for ; Tue, 6 Aug 2019 02:29:17 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from pylon.nyi.freebsd.org (pylon.nyi.freebsd.org [IPv6:2610:1c1:1:6082::16:fc]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 5E8B2252B5 for ; Tue, 6 Aug 2019 02:29:17 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from pylon.nyi.freebsd.org (localhost [127.0.0.1]) by pylon.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id x762THxP087300 for ; Tue, 6 Aug 2019 02:29:17 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by pylon.nyi.freebsd.org (8.15.2/8.15.2/Submit) id x762THMn087292; Tue, 6 Aug 2019 02:29:17 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Tue, 6 Aug 2019 02:29:17 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201908060229.x762THMn087292@pylon.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 120powerpc64-quarterly][biology/hhsuite] Failed for hhsuite-3.2.0 in build X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 06 Aug 2019 02:29:17 -0000 X-List-Received-Date: Tue, 06 Aug 2019 02:29:17 -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: yuri@FreeBSD.org Ident: $FreeBSD: branches/2019Q3/biology/hhsuite/Makefile 502244 2019-05-22 02:50:56Z yuri $ Log URL: http://pylon.nyi.freebsd.org/data/120powerpc64-quarterly/508200/logs/hhsuite-3.2.0.log Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=120powerpc64-quarterly&build=508200 Log: =>> Building biology/hhsuite build started at Tue Aug 6 02:28:03 UTC 2019 port directory: /usr/ports/biology/hhsuite package name: hhsuite-3.2.0 building for: FreeBSD 120powerpc64-quarterly-job-09 12.0-RELEASE-p8 FreeBSD 12.0-RELEASE-p8 1200086 powerpc maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: branches/2019Q3/biology/hhsuite/Makefile 502244 2019-05-22 02:50:56Z yuri $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300037 Jail OSVERSION: 1200086 Job Id: 09 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p8 1200086 UNAME_r=12.0-RELEASE-p8 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/120powerpc64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/120powerpc64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=120powerpc64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/120powerpc64-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/python3.6" 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/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=freebsd12 PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2 PERL_VER=5.28 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/5.28 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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_921dbbb2=none ARCH=powerpc64 OPSYS=FreeBSD _OSRELEASE=12.0-RELEASE-p8 OSREL=12.0 OSVERSION=1200086 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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) 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 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz [120powerpc64-quarterly-job-09] Installing pkg-1.11.1... [120powerpc64-quarterly-job-09] Extracting pkg-1.11.1: .......... done ===> hhsuite-3.2.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hhsuite-3.2.0 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hhsuite-3.2.0 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hhsuite-3.2.0 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 for building ===> Extracting for hhsuite-3.2.0 => SHA256 Checksum OK for soedinglab-hh-suite-v3.2.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for hhsuite-3.2.0 ===> Applying FreeBSD patches for hhsuite-3.2.0 =========================================================================== =================================================== ===> hhsuite-3.2.0 depends on package: openmpi>0 - not found ===> Installing existing package /packages/All/openmpi-1.10.7_5.txz [120powerpc64-quarterly-job-09] Installing openmpi-1.10.7_5... [120powerpc64-quarterly-job-09] `-- Installing gcc8-8.3.0_2... [120powerpc64-quarterly-job-09] | `-- Installing binutils-2.32_1,1... [120powerpc64-quarterly-job-09] | | `-- Installing gettext-runtime-0.20.1... [120powerpc64-quarterly-job-09] | | `-- Installing indexinfo-0.3.1... [120powerpc64-quarterly-job-09] | | `-- Extracting indexinfo-0.3.1: .... done [120powerpc64-quarterly-job-09] | | `-- Extracting gettext-runtime-0.20.1: .......... done [120powerpc64-quarterly-job-09] | `-- Extracting binutils-2.32_1,1: .......... done [120powerpc64-quarterly-job-09] | `-- Installing gmp-6.1.2_1... [120powerpc64-quarterly-job-09] | `-- Extracting gmp-6.1.2_1: .......... done [120powerpc64-quarterly-job-09] | `-- Installing mpc-1.1.0_2... [120powerpc64-quarterly-job-09] | | `-- Installing mpfr-4.0.2... of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from perl5-5.28.2: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> hhsuite-3.2.0 depends on package: openmpi>0 - found ===> Returning to build of hhsuite-3.2.0 ===> hhsuite-3.2.0 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.14.5.txz [120powerpc64-quarterly-job-09] Installing cmake-3.14.5... [120powerpc64-quarterly-job-09] `-- Installing curl-7.65.1... [120powerpc64-quarterly-job-09] | `-- Installing ca_root_nss-3.45... [120powerpc64-quarterly-job-09] | `-- Extracting ca_root_nss-3.45: ........ done [120powerpc64-quarterly-job-09] | `-- Installing libnghttp2-1.39.1... [120powerpc64-quarterly-job-09] | `-- Extracting libnghttp2-1.39.1: .......... done [120powerpc64-quarterly-job-09] `-- Extracting curl-7.65.1: .......... done [120powerpc64-quarterly-job-09] `-- Installing expat-2.2.6_1... [120powerpc64-quarterly-job-09] `-- Extracting expat-2.2.6_1: .......... done [120powerpc64-quarterly-job-09] `-- Installing jsoncpp-1.8.1_6... [120powerpc64-quarterly-job-09] `-- Extracting jsoncpp-1.8.1_6: .......... done [120powerpc64-quarterly-job-09] `-- Installing libarchive-3.3.3,1... [120powerpc64-quarterly-job-09] | `-- Installing lzo2-2.10_1... [120powerpc64-quarterly-job-09] | `-- Extracting lzo2-2.10_1: .......... done [120powerpc64-quarterly-job-09] `-- Extracting libarchive-3.3.3,1: .......... done [120powerpc64-quarterly-job-09] `-- Installing libuv-1.30.1... [120powerpc64-quarterly-job-09] `-- Extracting libuv-1.30.1: .......... done [120powerpc64-quarterly-job-09] `-- Installing rhash-1.3.5... [120powerpc64-quarterly-job-09] `-- Extracting rhash-1.3.5: .......... done [120powerpc64-quarterly-job-09] Extracting cmake-3.14.5: .......... done Message from ca_root_nss-3.45: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> hhsuite-3.2.0 depends on file: /usr/local/bin/cmake - found ===> Returning to build of hhsuite-3.2.0 ===> hhsuite-3.2.0 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.9.0,2.txz [120powerpc64-quarterly-job-09] Installing ninja-1.9.0,2... [120powerpc64-quarterly-job-09] `-- Installing python36-3.6.9... [120powerpc64-quarterly-job-09] | `-- Installing libffi-3.2.1_3... [120powerpc64-quarterly-job-09] | `-- Extracting libffi-3.2.1_3: .......... done [120powerpc64-quarterly-job-09] `-- Extracting python36-3.6.9: .......... done [120powerpc64-quarterly-job-09] Extracting ninja-1.9.0,2: ......... done Message from python36-3.6.9: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== ===> hhsuite-3.2.0 depends on executable: ninja - found ===> Returning to build of hhsuite-3.2.0 ===> hhsuite-3.2.0 depends on file: /usr/local/bin/python3.6 - found ===> hhsuite-3.2.0 depends on package: perl5>=5.28.r1<5.29 - found =========================================================================== =================================================== ===> hhsuite-3.2.0 depends on shared library: libomp.so - not found ===> Installing existing package /packages/All/openmp-8.0.0_1.txz [120powerpc64-quarterly-job-09] Installing openmp-8.0.0_1... [120powerpc64-quarterly-job-09] Extracting openmp-8.0.0_1: .......... done Message from openmp-8.0.0_1: ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Part of base system since FreeBSD 11.3/12.1. It is scheduled to be removed on or after 2020-02-01. ===> hhsuite-3.2.0 depends on shared library: libomp.so - found (/usr/local/lib/libomp.so) ===> Returning to build of hhsuite-3.2.0 =========================================================================== =================================================== ===> Configuring for hhsuite-3.2.0 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build -- The C compiler identification is GNU 4.2.1 -- The CXX compiler identification is GNU 4.2.1 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for fmemopen -- Looking for fmemopen - found -- Found MPI_C: /usr/local/mpi/openmpi/lib/libmpi.so (found version "3.0") -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_CXX_FOUND) (found version "3.0") -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_CXX_FOUND) (found version "3.0") -- xxd not found, using xxdi.pl instead -- SIMD: No HAVE_AVX2 or HAVE_SSE2 are set, trying to detect them -- Using CPU native flags for SSE optimization: -march=native -- Performing Test HAVE_MM_MALLOC -- Performing Test HAVE_MM_MALLOC - Failed -- Performing Test HAVE_POSIX_MEMALIGN -- Performing Test HAVE_POSIX_MEMALIGN - Failed -- Performing Test HAVE_AVX2_EXTENSIONS -- Performing Test HAVE_AVX2_EXTENSIONS - Failed -- Performing Test HAVE_AVX_EXTENSIONS -- Performing Test HAVE_AVX_EXTENSIONS - Failed -- Performing Test HAVE_SSE4_2_EXTENSIONS -- Performing Test HAVE_SSE4_2_EXTENSIONS - Failed -- Performing Test HAVE_SSE4_1_EXTENSIONS -- Performing Test HAVE_SSE4_1_EXTENSIONS - Failed -- Performing Test HAVE_SSSE3_EXTENSIONS -- Performing Test HAVE_SSSE3_EXTENSIONS - Failed -- Performing Test HAVE_SSE3_EXTENSIONS -- Performing Test HAVE_SSE3_EXTENSIONS - Failed -- Performing Test HAVE_SSE2_EXTENSIONS -- Performing Test HAVE_SSE2_EXTENSIONS - Failed -- Performing Test HAVE_SSE_EXTENSIONS -- Performing Test HAVE_SSE_EXTENSIONS - Failed -- No SSE extensions found -- SIMD: This platform doesn't have a supported SIMD instruction set, expect it to be slow. -- Found OpenMP_C: -fopenmp (found version "2.5") -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_CXX_FOUND) (found version "2.5") -- 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 [1/96] /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 -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 [2/96] /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 [3/96] /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 [4/96] /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 [5/96] : && /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 && : [6/96] : && /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/gcc8 -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 -lmpq /usr/local/mpi/openmpi/lib/libmpi.so && : FAILED: lib/ffindex/src/ffindex_apply_mpi : && /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/gcc8 -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 -lmpq /usr/local/mpi/openmpi/lib/libmpi.so && : /usr/bin/ld: cannot find -lmpq ninja: build stopped: subcommand failed. *** Error code 1 Stop. make: stopped in /usr/ports/biology/hhsuite