Date: Wed, 13 Jun 2018 03:49:28 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 111arm64-default][biology/unanimity] Failed for unanimity-g20180307 in build Message-ID: <201806130349.w5D3nSdT004247@thunderx1.nyi.freebsd.org>
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Maintainer: jwb@FreeBSD.org Last committer: jwb@FreeBSD.org Ident: $FreeBSD: head/biology/unanimity/Makefile 468214 2018-04-24 14:16:46Z jwb $ Log URL: http://thunderx1.nyi.freebsd.org/data/111arm64-default/471899/logs/unanimity-g20180307.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=111arm64-default&build=471899 Log: =>> Building biology/unanimity build started at Wed Jun 13 03:23:07 UTC 2018 port directory: /usr/ports/biology/unanimity package name: unanimity-g20180307 building for: FreeBSD 111arm64-default-job-20 11.1-RELEASE FreeBSD 11.1-RELEASE arm64 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/unanimity/Makefile 468214 2018-04-24 14:16:46Z jwb $ Poudriere version: 3.2.7 Host OSVERSION: 1200060 Jail OSVERSION: 1101001 Job Id: 20 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1101001 UNAME_v=FreeBSD 11.1-RELEASE UNAME_r=11.1-RELEASE 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=3.2.7 MASTERMNT=/usr/local/poudriere/data/.m/111arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/111arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=111arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/111arm64-default/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-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/unanimity/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/unanimity/work HOME=/wrkdirs/usr/ports/biology/unanimity/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/unanimity/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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/unanimity/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/unanimity/work HOME=/wrkdirs/usr/ports/biology/unanimity/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/unanimity/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/unanimity/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -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-- PORTDOCS="" PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd11 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=11.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/unanimity" EXAMPLESDIR="share/examples/unanimity" DATADIR="share/unanimity" WWWDIR="www/unanimity" ETCDIR="etc/unanimity" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/unanimity DOCSDIR=/usr/local/share/doc/unanimity EXAMPLESDIR=/usr/local/share/examples/unanimity WWWDIR=/usr/local/www/unanimity ETCDIR=/usr/local/etc/unanimity --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. 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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 4.0.0 (tags/RELEASE_400/final 297347) (based on LLVM 4.0.0) Target: aarch64-unknown-freebsd11.1 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 4.0.0 (tags/RELEASE_400/final 297347) (based on LLVM 4.0.0) Target: aarch64-unknown-freebsd11.1 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_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 4.0.0 (tags/RELEASE_400/final 297347) (based on LLVM 4.0.0) Target: aarch64-unknown-freebsd11.1 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=11.1-RELEASE OSREL=11.1 OSVERSION=1101001 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) 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-- =======================<phase: check-sanity >============================ ===> License BSD3CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> unanimity-g20180307 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz [111arm64-default-job-20] Installing pkg-1.10.5_1... [111arm64-default-job-20] Extracting pkg-1.10.5_1: .......... done ===> unanimity-g20180307 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of unanimity-g20180307 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE accepted by the user => PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/PacificBiosciences/unanimity/tar.gz/6f11a13e1472b8c00337ba8c5e94bf83bdab31d6?dummy=/PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6_GH0.tar.gz fetch: https://codeload.github.com/PacificBiosciences/unanimity/tar.gz/6f11a13e1472b8c00337ba8c5e94bf83bdab31d6?dummy=/PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6_GH0.tar.gz: size unknown fetch: https://codeload.github.com/PacificBiosciences/unanimity/tar.gz/6f11a13e1472b8c00337ba8c5e94bf83bdab31d6?dummy=/PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6_GH0.tar.gz: size of remote file is not known PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c 0 B 0 Bps ===> Fetching all distfiles required by unanimity-g20180307 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by unanimity-g20180307 for building => SHA256 Checksum OK for PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by unanimity-g20180307 for building ===> Extracting for unanimity-g20180307 => SHA256 Checksum OK for PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for unanimity-g20180307 ===> Applying FreeBSD patches for unanimity-g20180307 =========================================================================== =======================<phase: build-depends >============================ ===> unanimity-g20180307 depends on package: pbseqan==g20171002 - not found ===> Installing existing package /packages/All/pbseqan-g20171002.txz [111arm64-default-job-20] Installing pbseqan-g20171002... [111arm64-default-job-20] Extracting pbseqan-g20171002: .......... done ===> unanimity-g20180307 depends on package: pbseqan==g20171002 - found ===> Returning to build of unanimity-g20180307 ===> unanimity-g20180307 depends on package: pbbam==g20180416 - not found ===> Installing existing package /packages/All/pbbam-g20180416.txz [111arm64-default-job-20] Installing pbbam-g20180416... [111arm64-default-job-20] `-- Installing boost-libs-1.67.0_1... [111arm64-default-job-20] | `-- Installing icu-61.1,1... [111arm64-default-job-20] | `-- Extracting icu-61.1,1: .......... done [111arm64-default-job-20] `-- Extracting boost-libs-1.67.0_1: .......... done [111arm64-default-job-20] `-- Installing htslib-1.6... [111arm64-default-job-20] | `-- Installing curl-7.60.0... [111arm64-default-job-20] | | `-- Installing ca_root_nss-3.37.3... [111arm64-default-job-20] | | `-- Extracting ca_root_nss-3.37.3: ........ done [111arm64-default-job-20] | | `-- Installing libnghttp2-1.32.0... <snip> [9/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/matrix/BasicDenseMatrix.cpp.o -MF src/CMakeFiles/cc2.dir/matrix/BasicDenseMatrix.cpp.o.d -o src/CMakeFiles/cc2.dir/matrix/BasicDenseMatrix.cpp.o -c src/matrix/BasicDenseMatrix.cpp [10/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 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-std=c++14 -MD -MT src/CMakeFiles/cc2.dir/poa/PoaGraphImpl.cpp.o -MF src/CMakeFiles/cc2.dir/poa/PoaGraphImpl.cpp.o.d -o src/CMakeFiles/cc2.dir/poa/PoaGraphImpl.cpp.o -c src/poa/PoaGraphImpl.cpp [25/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/poa/PoaGraphTraversals.cpp.o -MF src/CMakeFiles/cc2.dir/poa/PoaGraphTraversals.cpp.o.d -o src/CMakeFiles/cc2.dir/poa/PoaGraphTraversals.cpp.o -c src/poa/PoaGraphTraversals.cpp [26/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/poa/RangeFinder.cpp.o -MF src/CMakeFiles/cc2.dir/poa/RangeFinder.cpp.o.d -o src/CMakeFiles/cc2.dir/poa/RangeFinder.cpp.o -c src/poa/RangeFinder.cpp [27/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/Coverage.cpp.o -MF src/CMakeFiles/cc2.dir/Coverage.cpp.o.d -o src/CMakeFiles/cc2.dir/Coverage.cpp.o -c src/Coverage.cpp [28/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/EasyReadScorer.cpp.o -MF src/CMakeFiles/cc2.dir/EasyReadScorer.cpp.o.d -o src/CMakeFiles/cc2.dir/EasyReadScorer.cpp.o -c src/EasyReadScorer.cpp [29/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/Evaluator.cpp.o -MF src/CMakeFiles/cc2.dir/Evaluator.cpp.o.d -o src/CMakeFiles/cc2.dir/Evaluator.cpp.o -c src/Evaluator.cpp [30/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/EvaluatorImpl.cpp.o -MF src/CMakeFiles/cc2.dir/EvaluatorImpl.cpp.o.d -o src/CMakeFiles/cc2.dir/EvaluatorImpl.cpp.o -c src/EvaluatorImpl.cpp [31/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/Integrator.cpp.o -MF src/CMakeFiles/cc2.dir/Integrator.cpp.o.d -o src/CMakeFiles/cc2.dir/Integrator.cpp.o -c src/Integrator.cpp [32/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/IntervalMask.cpp.o -MF src/CMakeFiles/cc2.dir/IntervalMask.cpp.o.d -o src/CMakeFiles/cc2.dir/IntervalMask.cpp.o -c src/IntervalMask.cpp [33/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/ModelConfig.cpp.o -MF src/CMakeFiles/cc2.dir/ModelConfig.cpp.o.d -o src/CMakeFiles/cc2.dir/ModelConfig.cpp.o -c src/ModelConfig.cpp [34/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/ModelFactory.cpp.o -MF src/CMakeFiles/cc2.dir/ModelFactory.cpp.o.d -o src/CMakeFiles/cc2.dir/ModelFactory.cpp.o -c src/ModelFactory.cpp [35/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/ModelFormFactory.cpp.o -MF src/CMakeFiles/cc2.dir/ModelFormFactory.cpp.o.d -o src/CMakeFiles/cc2.dir/ModelFormFactory.cpp.o -c src/ModelFormFactory.cpp [36/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/ModelSelection.cpp.o -MF src/CMakeFiles/cc2.dir/ModelSelection.cpp.o.d -o src/CMakeFiles/cc2.dir/ModelSelection.cpp.o -c src/ModelSelection.cpp [37/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/Mutation.cpp.o -MF src/CMakeFiles/cc2.dir/Mutation.cpp.o.d -o src/CMakeFiles/cc2.dir/Mutation.cpp.o -c src/Mutation.cpp In file included from src/Mutation.cpp:9: In file included from include/pacbio/consensus/Mutation.h:14: In file included from /usr/local/include/boost/optional.hpp:15: In file included from /usr/local/include/boost/optional/optional.hpp:45: In file included from /usr/local/include/boost/type_traits/is_constructible.hpp:17: /usr/local/include/boost/type_traits/is_destructible.hpp:29:51: warning: destructor called on non-final 'PacBio::Consensus::Mutation' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] template<typename T, typename = decltype(boost::declval<T&>().~T())> ^ /usr/local/include/boost/type_traits/is_constructible.hpp:54:99: note: in instantiation of template class 'boost::is_destructible<PacBio::Consensus::Mutation>' requested here template <class T, class Arg> struct is_constructible<T, Arg> : public integral_constant<bool, is_destructible<T>::value && sizeof(detail::is_constructible_imp::test1<T, Arg>(0)) == sizeof(boost::type_traits::yes_type)> ^ /usr/local/include/boost/optional/optional.hpp:785:36: note: in instantiation of template class 'boost::is_constructible<PacBio::Consensus::Mutation, const PacBio::Consensus::Mutation &>' requested here struct is_optional_constructible : boost::is_constructible<T, U> ^ /usr/local/include/boost/core/enable_if.hpp:41:41: note: in instantiation of template class 'boost::optional_detail::is_optional_constructible<PacBio::Consensus::Mutation, const PacBio::Consensus::Mutation &>' requested here struct enable_if : public enable_if_c<Cond::value, T> {}; ^ /usr/local/include/boost/optional/optional.hpp:887:56: note: in instantiation of template class 'boost::enable_if<boost::optional_detail::is_optional_constructible<PacBio::Consensus::Mutation, const PacBio::Consensus::Mutation &>, bool>' requested here ,BOOST_DEDUCED_TYPENAME boost::enable_if< optional_detail::is_optional_constructible<T, U const&>, bool>::type = true ^ src/Mutation.cpp:47:9: note: while substituting deduced template arguments into function template 'optional' [with U = PacBio::Consensus::Mutation] return boost::none; ^ /usr/local/include/boost/type_traits/is_destructible.hpp:29:73: note: qualify call to silence this warning template<typename T, typename = decltype(boost::declval<T&>().~T())> ^ PacBio::Consensus::Mutation:: 1 warning generated. [38/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/Polish.cpp.o -MF src/CMakeFiles/cc2.dir/Polish.cpp.o.d -o src/CMakeFiles/cc2.dir/Polish.cpp.o -c src/Polish.cpp In file included from src/Polish.cpp:14: In file included from /usr/local/include/boost/math/distributions/chi_squared.hpp:13: In file included from /usr/local/include/boost/math/special_functions/gamma.hpp:24: In file included from /usr/local/include/boost/math/constants/constants.hpp:13: In file included from /usr/local/include/boost/math/tools/convert_from_string.hpp:13: In file included from /usr/local/include/boost/type_traits/is_constructible.hpp:17: /usr/local/include/boost/type_traits/is_destructible.hpp:29:51: warning: destructor called on non-final 'PacBio::Consensus::ScoredMutation' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] template<typename T, typename = decltype(boost::declval<T&>().~T())> ^ /usr/local/include/boost/type_traits/is_constructible.hpp:54:99: note: in instantiation of template class 'boost::is_destructible<PacBio::Consensus::ScoredMutation>' requested here template <class T, class Arg> struct is_constructible<T, Arg> : public integral_constant<bool, is_destructible<T>::value && sizeof(detail::is_constructible_imp::test1<T, Arg>(0)) == sizeof(boost::type_traits::yes_type)> ^ /usr/local/include/boost/optional/optional.hpp:785:36: note: in instantiation of template class 'boost::is_constructible<PacBio::Consensus::ScoredMutation, const PacBio::Consensus::ScoredMutation &>' requested here struct is_optional_constructible : boost::is_constructible<T, U> ^ /usr/local/include/boost/core/enable_if.hpp:41:41: note: in instantiation of template class 'boost::optional_detail::is_optional_constructible<PacBio::Consensus::ScoredMutation, const PacBio::Consensus::ScoredMutation &>' requested here struct enable_if : public enable_if_c<Cond::value, T> {}; ^ /usr/local/include/boost/optional/optional.hpp:887:56: note: in instantiation of template class 'boost::enable_if<boost::optional_detail::is_optional_constructible<PacBio::Consensus::ScoredMutation, const PacBio::Consensus::ScoredMutation &>, bool>' requested here ,BOOST_DEDUCED_TYPENAME boost::enable_if< optional_detail::is_optional_constructible<T, U const&>, bool>::type = true ^ src/Polish.cpp:395:41: note: while substituting deduced template arguments into function template 'optional' [with U = PacBio::Consensus::ScoredMutation] boost::optional<ScoredMutation> bestMut = boost::none; ^ /usr/local/include/boost/type_traits/is_destructible.hpp:29:73: note: qualify call to silence this warning template<typename T, typename = decltype(boost::declval<T&>().~T())> ^ PacBio::Consensus::ScoredMutation:: 1 warning generated. [39/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/PolishResult.cpp.o -MF src/CMakeFiles/cc2.dir/PolishResult.cpp.o.d -o src/CMakeFiles/cc2.dir/PolishResult.cpp.o -c src/PolishResult.cpp [40/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/Read.cpp.o -MF src/CMakeFiles/cc2.dir/Read.cpp.o.d -o src/CMakeFiles/cc2.dir/Read.cpp.o -c src/Read.cpp [41/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/Recursor.cpp.o -MF src/CMakeFiles/cc2.dir/Recursor.cpp.o.d -o src/CMakeFiles/cc2.dir/Recursor.cpp.o -c src/Recursor.cpp [42/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/Sequence.cpp.o -MF src/CMakeFiles/cc2.dir/Sequence.cpp.o.d -o src/CMakeFiles/cc2.dir/Sequence.cpp.o -c src/Sequence.cpp [43/82] /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/cc2.dir/Template.cpp.o -MF src/CMakeFiles/cc2.dir/Template.cpp.o.d -o src/CMakeFiles/cc2.dir/Template.cpp.o -c src/Template.cpp [44/82] : && /usr/local/bin/cmake -E remove src/libcc2.a && /usr/bin/ar qc src/libcc2.a src/CMakeFiles/cc2.dir/__/generated/UnanimityGitHash.cpp.o src/CMakeFiles/cc2.dir/__/generated/UnanimityVersion.cpp.o src/CMakeFiles/cc2.dir/__/generated/ModelInternalInitializer.cpp.o src/CMakeFiles/cc2.dir/align/AffineAlignment.cpp.o src/CMakeFiles/cc2.dir/align/AlignConfig.cpp.o src/CMakeFiles/cc2.dir/align/BandedChainAlignment.cpp.o 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-fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/__/third-party/cssw/ssw_cpp.cpp.o -MF src/CMakeFiles/unanimity.dir/__/third-party/cssw/ssw_cpp.cpp.o.d -o src/CMakeFiles/unanimity.dir/__/third-party/cssw/ssw_cpp.cpp.o -c third-party/cssw/ssw_cpp.cpp FAILED: src/CMakeFiles/unanimity.dir/__/third-party/cssw/ssw_cpp.cpp.o /usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/__/third-party/cssw/ssw_cpp.cpp.o -MF src/CMakeFiles/unanimity.dir/__/third-party/cssw/ssw_cpp.cpp.o.d -o src/CMakeFiles/unanimity.dir/__/third-party/cssw/ssw_cpp.cpp.o -c third-party/cssw/ssw_cpp.cpp In file included from third-party/cssw/ssw_cpp.cpp:2: In file included from third-party/cssw/ssw.h:17: In file included from /usr/bin/../lib/clang/4.0.0/include/emmintrin.h:27: In file included from /usr/bin/../lib/clang/4.0.0/include/xmmintrin.h:27: /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:47:5: error: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'? __builtin_ia32_emms(); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:47:5: note: '__builtin_isless' declared here /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:47:25: error: too few arguments to function call, expected 2, have 0 __builtin_ia32_emms(); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:64:19: error: use of undeclared identifier '__builtin_ia32_vec_init_v2si' return (__m64)__builtin_ia32_vec_init_v2si(__i, 0); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:81:12: error: use of undeclared identifier '__builtin_ia32_vec_ext_v2si' return __builtin_ia32_vec_ext_v2si((__v2si)__m, 0); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:143:19: error: use of undeclared identifier '__builtin_ia32_packsswb' return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:173:19: error: use of undeclared identifier '__builtin_ia32_packssdw' return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:203:19: error: use of undeclared identifier '__builtin_ia32_packuswb' return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:230:19: error: use of undeclared identifier '__builtin_ia32_punpckhbw' return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:253:19: error: use of undeclared identifier '__builtin_ia32_punpckhwd' return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:274:19: error: use of undeclared identifier '__builtin_ia32_punpckhdq' return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:301:19: error: use of undeclared identifier '__builtin_ia32_punpcklbw' return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:324:19: error: use of undeclared identifier '__builtin_ia32_punpcklwd' return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:345:19: error: use of undeclared identifier '__builtin_ia32_punpckldq' return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:366:19: error: use of undeclared identifier '__builtin_ia32_paddb' return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:387:19: error: use of undeclared identifier '__builtin_ia32_paddw' return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:408:19: error: use of undeclared identifier '__builtin_ia32_paddd' return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:430:19: error: use of undeclared identifier '__builtin_ia32_paddsb' return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:453:19: error: use of undeclared identifier '__builtin_ia32_paddsw' return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2); ^ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:475:19: error: use of undeclared identifier '__builtin_ia32_paddusb' return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2); ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. ninja: build stopped: subcommand failed. *** Error code 1 Stop. make: stopped in /usr/ports/biology/unanimity
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