From nobody Sat Mar 12 22:22:44 2022 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 7269D1A12428 for ; Sat, 12 Mar 2022 22:22:44 +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 4KGHP01Qlwz3vHr for ; Sat, 12 Mar 2022 22:22:44 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy12.nyi.freebsd.org (beefy12.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:1b]) (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 1104557CF for ; Sat, 12 Mar 2022 22:22:44 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy12.nyi.freebsd.org (localhost [127.0.0.1]) by beefy12.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 22CMMi9L010140 for ; Sat, 12 Mar 2022 22:22:44 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy12.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 22CMMi9L010139; Sat, 12 Mar 2022 22:22:44 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 12 Mar 2022 22:22:44 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202203122222.22CMMi9L010139@beefy12.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 130releng-armv7-quarterly][biology/hhsuite] Failed for hhsuite-3.3.0 in build ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1647123764; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=OrwsjsyX43igkRUHjtQEotR5Cgo+HxpEA098QcwPlzU=; b=nsRo1EFbn5T6RMcUyZwebf8zCsEljTDsj8l1Ra5k3Uk3DNLqGqP7tPccIf02ODZjlQYED/ YTcMnK02NsAHfLqq0fSz2uNMn6VPpwYKQzp96IW2xX2/3t5urcne/DKE5eqqtT3tiWuEFj 8p4frP/bv7ZNjjAGubecnGQVvSM2eWqraDqXGs0WpLQZWe4Ukqup3FGecSZTSrWqB++tqJ xfYKJkmEMTKQ8H80ZBL11v4dTcs09hR11lNeg6+IqhOuNyXfyNjWaJUL2X5wvv0ce40LXQ FD/FqkFXFJHhLP/uyl0L/bz++OVRbQjpq1UcO8tjPlGZPl8jTw+COHJkQRvC4A== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1647123764; a=rsa-sha256; cv=none; b=IJfy/dDGLEhj6XeNLIkHg+1hsv5vOvZX2mfzC9rY/jS2cqjAFrxStCib1Ard1t1Kq6GuqP Yp4Gss73hizL1MIDIoGGwFPD8auHF1IMReMjbJNE5Cn4UtL6CvkW1yqEAOEfDV9hz3S/VB xO3L3JjGx0L3i69hmlqI0AjOQ0KA77Uh9IscEIt3QYxl+TAcfsV7RT3EQxAI9zgrr1rWxg PEDWLCv0qAAPfYNlCCZshxYAGjG6mNJvbVxEc25w8GZtLEgtDCuLTjIfk5JeGMLk8wyN7e iL52/eIoNhD84p83cK2jaqlxOv8YMSsBPxttn1Mjxi/OJLgGQmlgStT2Hy5BnQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N 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: http://beefy12.nyi.freebsd.org/data/130releng-armv7-quarterly/1b4a6a151c20/logs/hhsuite-3.3.0.log Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=130releng-armv7-quarterly&build=1b4a6a151c20 Log: =>> Building biology/hhsuite build started at Sat Mar 12 22:21:41 UTC 2022 port directory: /usr/ports/biology/hhsuite package name: hhsuite-3.3.0 building for: FreeBSD 130releng-armv7-quarterly-job-01 13.0-RELEASE-p7 FreeBSD 13.0-RELEASE-p7 1300139 arm maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400050 Jail OSVERSION: 1300139 Job Id: 01 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1300139 UNAME_v=FreeBSD 13.0-RELEASE-p7 1300139 UNAME_r=13.0-RELEASE-p7 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 LOCALBASE=/usr/local QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-21-g883afb07 MASTERMNT=/usr/local/poudriere/data/.m/130releng-armv7-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/130releng-armv7-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=130releng-armv7-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/130releng-armv7-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/python3.8" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/hhsuite/work/.cache 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-- NINJA_STATUS="[%p %s/%t] " PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/hhsuite/work/.cache 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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTA LL_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-- OPENMP="" CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.8 PYTHON_LIBDIR=lib/python3.8 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.8/site-packages PYTHON_SUFFIX=38 PYTHON_EXT_SUFFIX=.cpython-38 PYTHON_VER=3.8 PYTHON_VERSION=python3.8 PYTHON2="@comment " PYTHON3="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 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/5.32 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--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv7 ARCH=${MACHINE_ARCH} #### /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_9d218390=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--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_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=13.0-RELEASE-p7 OSREL=13.0 OSVERSION=1300139 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.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-3.3.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.5.pkg [130releng-armv7-quarterly-job-01] Installing pkg-1.17.5... [130releng-armv7-quarterly-job-01] Extracting pkg-1.17.5: .......... done ===> hhsuite-3.3.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hhsuite-3.3.0 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hhsuite-3.3.0 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hhsuite-3.3.0 for building => SHA256 Checksum OK for soedinglab-hh-suite-v3.3.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hhsuite-3.3.0 for building ===> Extracting for hhsuite-3.3.0 => SHA256 Checksum OK for soedinglab-hh-suite-v3.3.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for hhsuite-3.3.0 ===> Applying FreeBSD patches for hhsuite-3.3.0 from /usr/ports/biology/hhsuite/files =========================================================================== =================================================== ===> hhsuite-3.3.0 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.22.1.pkg [130releng-armv7-quarterly-job-01] Installing cmake-3.22.1... [130releng-armv7-quarterly-job-01] `-- Installing curl-7.80.0... [130releng-armv7-quarterly-job-01] | `-- Installing ca_root_nss-3.71... [130releng-armv7-quarterly-job-01] | `-- Extracting ca_root_nss-3.71: ........ done [130releng-armv7-quarterly-job-01] | `-- Installing libnghttp2-1.46.0... [130releng-armv7-quarterly-job-01] | `-- Extracting libnghttp2-1.46.0: .......... done [130releng-armv7-quarterly-job-01] | `-- Installing libssh2-1.10.0,3... [130releng-armv7-quarterly-job-01] | `-- Extracting libssh2-1.10.0,3: .......... done [130releng-armv7-quarterly-job-01] `-- Extracting curl-7.80.0: .......... done [130releng-armv7-quarterly-job-01] `-- Installing expat-2.4.7... [130releng-armv7-quarterly-job-01] `-- Extracting expat-2.4.7: .......... done [130releng-armv7-quarterly-job-01] `-- Installing jsoncpp-1.9.5... [130releng-armv7-quarterly-job-01] `-- Extracting jsoncpp-1.9.5: .......... done [130releng-armv7-quarterly-job-01] `-- Installing libarchive-3.5.2,1... [130releng-armv7-quarterly-job-01] | `-- Installing liblz4-1.9.3,1... [130releng-armv7-quarterly-job-01] | `-- Extracting liblz4-1.9.3,1: .......... done [130releng-armv7-quarterly-job-01] | `-- Installing zstd-1.5.0... [130releng-armv7-quarterly-job-01] | `-- Extracting zstd-1.5.0: .......... done [130releng-armv7-quarterly-job-01] `-- Extracting libarchive-3.5.2,1: .......... done [130releng-armv7-quarterly-job-01] `-- Installing libuv-1.42.0... [130releng-armv7-quarterly-job-01] `-- Extracting libuv-1.42.0: .......... done [130releng-armv7-quarterly-job-01] `-- Installing rhash-1.4.2... [130releng-armv7-quarterly-job-01] | `-- Installing gettext-runtime-0.21... [130releng-armv7-quarterly-job-01] | | `-- Installing indexinfo-0.3.1... [130releng-armv7-quarterly-job-01] | | `-- Extracting indexinfo-0.3.1: .... done [130releng-armv7-quarterly-job-01] | `-- Extracting gettext-runtime-0.21: .......... done [130releng-armv7-quarterly-job-01] `-- Extracting rhash-1.4.2: .......... done [130releng-armv7-quarterly-job-01] Extracting cmake-3.22.1: .......... done ===== Message from ca_root_nss-3.71: -- 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. 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-3.3.0 depends on file: /usr/local/bin/cmake - found ===> Returning to build of hhsuite-3.3.0 ===> hhsuite-3.3.0 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.10.2,2.pkg [130releng-armv7-quarterly-job-01] Installing ninja-1.10.2,2... [130releng-armv7-quarterly-job-01] `-- Installing python38-3.8.12_1... [130releng-armv7-quarterly-job-01] | `-- Installing libffi-3.3_1... [130releng-armv7-quarterly-job-01] | `-- Extracting libffi-3.3_1: .......... done [130releng-armv7-quarterly-job-01] | `-- Installing mpdecimal-2.5.1... [130releng-armv7-quarterly-job-01] | `-- Extracting mpdecimal-2.5.1: .......... done [130releng-armv7-quarterly-job-01] | `-- Installing readline-8.1.1... [130releng-armv7-quarterly-job-01] | `-- Extracting readline-8.1.1: .......... done [130releng-armv7-quarterly-job-01] `-- Extracting python38-3.8.12_1: .......... done [130releng-armv7-quarterly-job-01] Extracting ninja-1.10.2,2: ........ done ===== Message from python38-3.8.12_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py38-gdbm databases/py-gdbm@py38 py38-sqlite3 databases/py-sqlite3@py38 py38-tkinter x11-toolkits/py-tkinter@py38 ===> hhsuite-3.3.0 depends on executable: ninja - found ===> Returning to build of hhsuite-3.3.0 ===> hhsuite-3.3.0 depends on file: /usr/local/bin/python3.8 - found ===> hhsuite-3.3.0 depends on package: perl5>=5.32.r0<5.33 - not found ===> Installing existing package /packages/All/perl5-5.32.1_1.pkg [130releng-armv7-quarterly-job-01] Installing perl5-5.32.1_1... [130releng-armv7-quarterly-job-01] Extracting perl5-5.32.1_1: .......... done ===> hhsuite-3.3.0 depends on package: perl5>=5.32.r0<5.33 - found ===> Returning to build of hhsuite-3.3.0 =========================================================================== =================================================== ===> hhsuite-3.3.0 depends on shared library: libmpi.so - not found ===> Installing existing package /packages/All/openmpi-4.1.1.pkg [130releng-armv7-quarterly-job-01] Installing openmpi-4.1.1... [130releng-armv7-quarterly-job-01] `-- Installing gcc10-10.3.0... [130releng-armv7-quarterly-job-01] | `-- Installing binutils-2.37_2,1... [130releng-armv7-quarterly-job-01] | `-- Extracting binutils-2.37_2,1: .......... done [130releng-armv7-quarterly-job-01] | `-- Installing gmp-6.2.1... [130releng-armv7-quarterly-job-01] | `-- Extracting gmp-6.2.1: .......... done [130releng-armv7-quarterly-job-01] | `-- Installing mpc-1.2.1... [130releng-armv7-quarterly-job-01] | | `-- Installing mpfr-4.1.0_1... [130releng-armv7-quarterly-job-01] | | `-- Extracting mpfr-4.1.0_1: .......... done [130releng-armv7-quarterly-job-01] | `-- Extracting mpc-1.2.1: ......... done [130releng-armv7-quarterly-job-01] `-- Extracting gcc10-10.3.0: .......... done [130releng-armv7-quarterly-job-01] `-- Installing hwloc2-2.5.0... [130releng-armv7-quarterly-job-01] | `-- Installing level-zero-1.7.4... [130releng-armv7-quarterly-job-01] | `-- Extracting level-zero-1.7.4: .......... done [130releng-armv7-quarterly-job-01] | `-- Installing libpciaccess-0.16... [130releng-armv7-quarterly-job-01] | | `-- Installing pciids-20211124... [130releng-armv7-quarterly-job-01] | | `-- Extracting pciids-20211124: ..... done [130releng-armv7-quarterly-job-01] | `-- Extracting libpciaccess-0.16: ......... done [130releng-armv7-quarterly-job-01] | `-- Installing libxml2-2.9.12... [130releng-armv7-quarterly-job-01] | `-- Extracting libxml2-2.9.12: .......... done [130releng-armv7-quarterly-job-01] `-- Extracting hwloc2-2.5.0: .......... done [130releng-armv7-quarterly-job-01] `-- Installing libevent-2.1.12... [130releng-armv7-quarterly-job-01] `-- Extracting libevent-2.1.12: .......... done [130releng-armv7-quarterly-job-01] `-- Installing libltdl-2.4.6... [130releng-armv7-quarterly-job-01] `-- Extracting libltdl-2.4.6: .......... done [130releng-armv7-quarterly-job-01] `-- Installing munge-0.5.14_1... [130releng-armv7-quarterly-job-01] `-- Extracting munge-0.5.14_1: ......... done [130releng-armv7-quarterly-job-01] Extracting openmpi-4.1.1: .......... done ===== Message from gcc10-10.3.0: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc10 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> hhsuite-3.3.0 depends on shared library: libmpi.so - found (/usr/local/mpi/openmpi/lib/libmpi.so) ===> Returning to build of hhsuite-3.3.0 =========================================================================== =================================================== ===> Configuring for hhsuite-3.3.0 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build -- The C compiler identification is Clang 11.0.1 -- The CXX compiler identification is Clang 11.0.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /nxb-bin/usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /nxb-bin/usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is clang(++) -- Looking for fmemopen -- Looking for fmemopen - found -- Found MPI_C: /usr/local/mpi/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/local/mpi/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- xxd not found, using xxdi.pl instead -- 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_CXX_FLAGS_DEBUG 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-3.3.0 [ 1% 1/98] cd /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/data && mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated && /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/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 [ 2% 2/98] /nxb-bin/usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -march=native -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhviterbialgorithm.cpp FAILED: src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o /nxb-bin/usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -march=native -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhviterbialgorithm.cpp c++: error: the clang compiler does not support '-march=native' ninja: build stopped: subcommand failed. *** Error code 1 Stop. make: stopped in /usr/ports/biology/hhsuite