Date: Wed, 27 Jun 2018 13:23:36 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-arm64-default][biology/unanimity] Failed for unanimity-g20180307 in build Message-ID: <201806271323.w5RDNaEY066671@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/head-arm64-default/p472730_s335353/logs/unanimity-g20180307.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=head-arm64-default&build=p472730_s335353 Log: =>> Building biology/unanimity build started at Wed Jun 27 12:45:40 UTC 2018 port directory: /usr/ports/biology/unanimity package name: unanimity-g20180307 building for: FreeBSD head-arm64-default-job-17 12.0-CURRENT FreeBSD 12.0-CURRENT 1200069 arm64 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/unanimity/Makefile 468214 2018-04-24 14:16:46Z jwb $ Poudriere version: 3.2.7-1-g7087c444 Host OSVERSION: 1200060 Jail OSVERSION: 1200069 Job Id: 17 !!! Jail is newer than host. (Jail: 1200069, Host: 1200060) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1200069 UNAME_v=FreeBSD 12.0-CURRENT 1200069 UNAME_r=12.0-CURRENT 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=3.2.7-1-g7087c444 MASTERMNT=/usr/local/poudriere/data/.m/head-arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-arm64-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=freebsd12 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=12.0 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. 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 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: aarch64-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: aarch64-unknown-freebsd12.0 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 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: aarch64-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=12.0-CURRENT OSREL=12.0 OSVERSION=1200069 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 [head-arm64-default-job-17] Installing pkg-1.10.5_1... [head-arm64-default-job-17] 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 ===> 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 [head-arm64-default-job-17] Installing pbseqan-g20171002... [head-arm64-default-job-17] 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 [head-arm64-default-job-17] Installing pbbam-g20180416... [head-arm64-default-job-17] `-- Installing boost-libs-1.67.0_1... <snip> __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end)); ^ /usr/include/c++/v1/vector:356:29: note: in instantiation of member function 'std::__1::__vector_base<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> >::__destruct_at_end' requested here void clear() _NOEXCEPT {__destruct_at_end(__begin_);} ^ /usr/include/c++/v1/vector:441:9: note: in instantiation of member function 'std::__1::__vector_base<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> >::clear' requested here clear(); ^ /usr/include/c++/v1/iterator:1425:74: note: in instantiation of member function 'std::__1::__vector_base<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> >::~__vector_base' requested here template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector; ^ /usr/include/c++/v1/memory:1860:64: note: qualify call to silence this warning _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ 1 warning generated. [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 [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:3: In file included from /usr/include/c++/v1/algorithm:643: /usr/include/c++/v1/memory:1860:58: warning: destructor called on non-final 'PacBio::Consensus::Mutation' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ /usr/include/c++/v1/memory:1727:18: note: in instantiation of member function 'std::__1::allocator<PacBio::Consensus::Mutation>::destroy' requested here {__a.destroy(__p);} ^ /usr/include/c++/v1/memory:1595:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<PacBio::Consensus::Mutation> >::__destroy<PacBio::Consensus::Mutation>' requested here {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);} ^ /usr/include/c++/v1/__split_buffer:296:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<PacBio::Consensus::Mutation> >::destroy<PacBio::Consensus::Mutation>' requested here __alloc_traits::destroy(__alloc(), __to_raw_pointer(--__end_)); ^ /usr/include/c++/v1/__split_buffer:141:10: note: in instantiation of member function 'std::__1::__split_buffer<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> &>::__destruct_at_end' requested here {__destruct_at_end(__new_last, false_type());} ^ /usr/include/c++/v1/__split_buffer:88:10: note: in instantiation of member function 'std::__1::__split_buffer<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> &>::__destruct_at_end' requested here {__destruct_at_end(__begin_);} ^ /usr/include/c++/v1/__split_buffer:341:5: note: in instantiation of member function 'std::__1::__split_buffer<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> &>::clear' requested here clear(); ^ /usr/include/c++/v1/vector:1628:49: note: in instantiation of member function 'std::__1::__split_buffer<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> &>::~__split_buffer' requested here __split_buffer<value_type, allocator_type&> __v(__recommend(size() + 1), size(), __a); ^ /usr/include/c++/v1/vector:1655:9: note: in instantiation of function template specialization 'std::__1::vector<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> >::__emplace_back_slow_path<PacBio::Consensus::Mutation>' requested here __emplace_back_slow_path(_VSTD::forward<_Args>(__args)...); ^ src/Polish.cpp:87:50: note: in instantiation of function template specialization 'std::__1::vector<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> >::emplace_back<PacBio::Consensus::Mutation>' requested here if (!containedWithin(last, j)) muts->emplace_back(Mutation::Insertion(i, j)); ^ /usr/include/c++/v1/memory:1860:64: note: qualify call to silence this warning _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ /usr/include/c++/v1/memory:1732:17: warning: destructor called on non-final 'PacBio::Consensus::ScoredMutation' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] __p->~_Tp(); ^ /usr/include/c++/v1/memory:1595:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::__list_node<PacBio::Consensus::ScoredMutation, void *> > >::__destroy<PacBio::Consensus::ScoredMutation>' requested here {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);} ^ /usr/include/c++/v1/list:1830:34: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::__list_node<PacBio::Consensus::ScoredMutation, void *> > >::destroy<PacBio::Consensus::ScoredMutation>' requested here __node_alloc_traits::destroy(__na, _VSTD::addressof(__np->__value_)); ^ /usr/include/c++/v1/list:2131:19: note: in instantiation of member function 'std::__1::list<PacBio::Consensus::ScoredMutation, std::__1::allocator<PacBio::Consensus::ScoredMutation> >::erase' requested here __i = erase(__i, __j); ^ src/Polish.cpp:181:21: note: in instantiation of function template specialization 'std::__1::list<PacBio::Consensus::ScoredMutation, std::__1::allocator<PacBio::Consensus::ScoredMutation> >::remove_if<(lambda at src/Polish.cpp:182:13)>' requested here scoredMuts->remove_if( ^ /usr/include/c++/v1/memory:1732:23: note: qualify call to silence this warning __p->~_Tp(); ^ 2 warnings 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 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-fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/ChemistryMapping.cpp.o -MF src/CMakeFiles/unanimity.dir/ChemistryMapping.cpp.o.d -o src/CMakeFiles/unanimity.dir/ChemistryMapping.cpp.o -c src/ChemistryMapping.cpp [68/82] /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/unanimity.dir/ChemistryTriple.cpp.o -MF src/CMakeFiles/unanimity.dir/ChemistryTriple.cpp.o.d -o src/CMakeFiles/unanimity.dir/ChemistryTriple.cpp.o -c src/ChemistryTriple.cpp [69/82] /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/unanimity.dir/Interval.cpp.o -MF src/CMakeFiles/unanimity.dir/Interval.cpp.o.d -o src/CMakeFiles/unanimity.dir/Interval.cpp.o -c src/Interval.cpp [70/82] /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/unanimity.dir/ReadId.cpp.o -MF src/CMakeFiles/unanimity.dir/ReadId.cpp.o.d -o src/CMakeFiles/unanimity.dir/ReadId.cpp.o -c src/ReadId.cpp [71/82] /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/unanimity.dir/SparsePoa.cpp.o -MF src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o.d -o src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o -c src/SparsePoa.cpp [72/82] /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/unanimity.dir/SubreadResultCounter.cpp.o -MF src/CMakeFiles/unanimity.dir/SubreadResultCounter.cpp.o.d -o src/CMakeFiles/unanimity.dir/SubreadResultCounter.cpp.o -c src/SubreadResultCounter.cpp [73/82] /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/unanimity.dir/Timer.cpp.o -MF src/CMakeFiles/unanimity.dir/Timer.cpp.o.d -o src/CMakeFiles/unanimity.dir/Timer.cpp.o -c src/Timer.cpp [74/82] /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/unanimity.dir/Utility.cpp.o -MF src/CMakeFiles/unanimity.dir/Utility.cpp.o.d -o src/CMakeFiles/unanimity.dir/Utility.cpp.o -c src/Utility.cpp [75/82] /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/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/lib/clang/6.0.0/include/emmintrin.h:27: In file included from /usr/lib/clang/6.0.0/include/xmmintrin.h:27: /usr/lib/clang/6.0.0/include/mmintrin.h:47:5: error: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'? __builtin_ia32_emms(); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:47:5: note: '__builtin_isless' declared here /usr/lib/clang/6.0.0/include/mmintrin.h:47:25: error: too few arguments to function call, expected 2, have 0 __builtin_ia32_emms(); ^ /usr/lib/clang/6.0.0/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/lib/clang/6.0.0/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/lib/clang/6.0.0/include/mmintrin.h:143:19: error: use of undeclared identifier '__builtin_ia32_packsswb' return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:173:19: error: use of undeclared identifier '__builtin_ia32_packssdw' return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:203:19: error: use of undeclared identifier '__builtin_ia32_packuswb' return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:230:19: error: use of undeclared identifier '__builtin_ia32_punpckhbw' return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:253:19: error: use of undeclared identifier '__builtin_ia32_punpckhwd' return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:274:19: error: use of undeclared identifier '__builtin_ia32_punpckhdq' return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:301:19: error: use of undeclared identifier '__builtin_ia32_punpcklbw' return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:324:19: error: use of undeclared identifier '__builtin_ia32_punpcklwd' return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:345:19: error: use of undeclared identifier '__builtin_ia32_punpckldq' return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:366:19: error: use of undeclared identifier '__builtin_ia32_paddb' return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:387:19: error: use of undeclared identifier '__builtin_ia32_paddw' return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:408:19: error: use of undeclared identifier '__builtin_ia32_paddd' return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:430:19: error: use of undeclared identifier '__builtin_ia32_paddsb' return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2); ^ /usr/lib/clang/6.0.0/include/mmintrin.h:453:19: error: use of undeclared identifier '__builtin_ia32_paddsw' return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2); ^ /usr/lib/clang/6.0.0/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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