Date: Sat, 28 Sep 2019 03:04:39 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 120armv7-quarterly][biology/unanimity] Failed for unanimity-3.4.1_1 in build Message-ID: <201909280304.x8S34df3090029@beefy13.nyi.freebsd.org>
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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: jwb@FreeBSD.org Last committer: jbeich@FreeBSD.org Ident: $FreeBSD: branches/2019Q3/biology/unanimity/Makefile 498698 2019-04-12 06:36:31Z jbeich $ Log URL: http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/513028/logs/unanimity-3.4.1_1.log Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=513028 Log: =>> Building biology/unanimity build started at Sat Sep 28 03:00:42 UTC 2019 port directory: /usr/ports/biology/unanimity package name: unanimity-3.4.1_1 building for: FreeBSD 120armv7-quarterly-job-11 12.0-RELEASE-p10 FreeBSD 12.0-RELEASE-p10 1200086 arm maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: branches/2019Q3/biology/unanimity/Makefile 498698 2019-04-12 06:36:31Z jbeich $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300040 Jail OSVERSION: 1200086 Job Id: 11 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p10 1200086 UNAME_r=12.0-RELEASE-p10 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 QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/120armv7-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/120armv7-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=120armv7-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/120armv7-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-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix /usr/local --mandir man --infodir share/info --buildtype release --strip _build --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 CMAKE_PREFIX_PATH="/usr/local" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 --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 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lexecinfo -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTAL L_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-- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd12 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--- .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 # 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_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-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 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=12.0-RELEASE-p10 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--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as 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-- =======================<phase: check-sanity >============================ ===> License BSD3CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> unanimity-3.4.1_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz [120armv7-quarterly-job-11] Installing pkg-1.11.1... [120armv7-quarterly-job-11] Extracting pkg-1.11.1: .......... done ===> unanimity-3.4.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of unanimity-3.4.1_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by unanimity-3.4.1_1 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by unanimity-3.4.1_1 for building => SHA256 Checksum OK for PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ <snip> /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. [35/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/Integrator.cpp.o' -MF 'src/25a6634@@unanimity@sha/Integrator.cpp.o.d' -o 'src/25a6634@@unanimity@sha/Integrator.cpp.o' -c ../src/Integrator.cpp In file included from ../src/Integrator.cpp:7: In file included from /usr/include/c++/v1/numeric:144: In file included from /usr/include/c++/v1/functional:487: /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/vector:413:25: 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(), _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. [36/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/IntervalMask.cpp.o' -MF 'src/25a6634@@unanimity@sha/IntervalMask.cpp.o.d' -o 'src/25a6634@@unanimity@sha/IntervalMask.cpp.o' -c ../src/IntervalMask.cpp [37/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/ModelConfig.cpp.o' -MF 'src/25a6634@@unanimity@sha/ModelConfig.cpp.o.d' -o 'src/25a6634@@unanimity@sha/ModelConfig.cpp.o' -c ../src/ModelConfig.cpp [38/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/ModelFactory.cpp.o' -MF 'src/25a6634@@unanimity@sha/ModelFactory.cpp.o.d' -o 'src/25a6634@@unanimity@sha/ModelFactory.cpp.o' -c ../src/ModelFactory.cpp [39/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/ModelFormFactory.cpp.o' -MF 'src/25a6634@@unanimity@sha/ModelFormFactory.cpp.o.d' -o 'src/25a6634@@unanimity@sha/ModelFormFactory.cpp.o' -c ../src/ModelFormFactory.cpp [40/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/ModelSelection.cpp.o' -MF 'src/25a6634@@unanimity@sha/ModelSelection.cpp.o.d' -o 'src/25a6634@@unanimity@sha/ModelSelection.cpp.o' -c ../src/ModelSelection.cpp [41/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/Mutation.cpp.o' -MF 'src/25a6634@@unanimity@sha/Mutation.cpp.o.d' -o 'src/25a6634@@unanimity@sha/Mutation.cpp.o' -c ../src/Mutation.cpp [42/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/Polish.cpp.o' -MF 'src/25a6634@@unanimity@sha/Polish.cpp.o.d' -o 'src/25a6634@@unanimity@sha/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. [43/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/PolishResult.cpp.o' -MF 'src/25a6634@@unanimity@sha/PolishResult.cpp.o.d' -o 'src/25a6634@@unanimity@sha/PolishResult.cpp.o' -c ../src/PolishResult.cpp [44/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/Read.cpp.o' -MF 'src/25a6634@@unanimity@sha/Read.cpp.o.d' -o 'src/25a6634@@unanimity@sha/Read.cpp.o' -c ../src/Read.cpp [45/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread 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-Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/Utility.cpp.o' -MF 'src/25a6634@@unanimity@sha/Utility.cpp.o.d' -o 'src/25a6634@@unanimity@sha/Utility.cpp.o' -c ../src/Utility.cpp [61/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/ConsensusSettings.cpp.o' -MF 'src/25a6634@@unanimity@sha/ConsensusSettings.cpp.o.d' -o 'src/25a6634@@unanimity@sha/ConsensusSettings.cpp.o' -c ../src/ConsensusSettings.cpp [62/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/LocalAlignment.cpp.o' -MF 'src/25a6634@@unanimity@sha/LocalAlignment.cpp.o.d' -o 'src/25a6634@@unanimity@sha/LocalAlignment.cpp.o' -c ../src/LocalAlignment.cpp [63/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/models_P6C4NoCov_Model.cpp.o' -MF 'src/25a6634@@unanimity@sha/models_P6C4NoCov_Model.cpp.o.d' -o 'src/25a6634@@unanimity@sha/models_P6C4NoCov_Model.cpp.o' -c ../src/models/P6C4NoCov_Model.cpp [64/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/models_S_P1C1Beta_Model.cpp.o' -MF 'src/25a6634@@unanimity@sha/models_S_P1C1Beta_Model.cpp.o.d' -o 'src/25a6634@@unanimity@sha/models_S_P1C1Beta_Model.cpp.o' -c ../src/models/S_P1C1Beta_Model.cpp [65/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/models_S_P1C1v1_Model.cpp.o' -MF 'src/25a6634@@unanimity@sha/models_S_P1C1v1_Model.cpp.o.d' -o 'src/25a6634@@unanimity@sha/models_S_P1C1v1_Model.cpp.o' -c ../src/models/S_P1C1v1_Model.cpp [66/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/models_S_P1C1v2_Model.cpp.o' -MF 'src/25a6634@@unanimity@sha/models_S_P1C1v2_Model.cpp.o.d' -o 'src/25a6634@@unanimity@sha/models_S_P1C1v2_Model.cpp.o' -c ../src/models/S_P1C1v2_Model.cpp [67/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/models_S_P2C2v5_Model.cpp.o' -MF 'src/25a6634@@unanimity@sha/models_S_P2C2v5_Model.cpp.o.d' -o 'src/25a6634@@unanimity@sha/models_S_P2C2v5_Model.cpp.o' -c ../src/models/S_P2C2v5_Model.cpp [68/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/models_MarginalModelForm.cpp.o' -MF 'src/25a6634@@unanimity@sha/models_MarginalModelForm.cpp.o.d' -o 'src/25a6634@@unanimity@sha/models_MarginalModelForm.cpp.o' -c ../src/models/MarginalModelForm.cpp [69/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/models_PwSnrAModelForm.cpp.o' -MF 'src/25a6634@@unanimity@sha/models_PwSnrAModelForm.cpp.o.d' -o 'src/25a6634@@unanimity@sha/models_PwSnrAModelForm.cpp.o' -c ../src/models/PwSnrAModelForm.cpp [70/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/models_PwSnrModelForm.cpp.o' -MF 'src/25a6634@@unanimity@sha/models_PwSnrModelForm.cpp.o.d' -o 'src/25a6634@@unanimity@sha/models_PwSnrModelForm.cpp.o' -c ../src/models/PwSnrModelForm.cpp [71/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/models_SnrModelForm.cpp.o' -MF 'src/25a6634@@unanimity@sha/models_SnrModelForm.cpp.o.d' -o 'src/25a6634@@unanimity@sha/models_SnrModelForm.cpp.o' -c ../src/models/SnrModelForm.cpp [72/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/meson-generated_.._ModelInternalInitializer.cpp.o' -MF 'src/25a6634@@unanimity@sha/meson-generated_.._ModelInternalInitializer.cpp.o.d' -o 'src/25a6634@@unanimity@sha/meson-generated_.._ModelInternalInitializer.cpp.o' -c src/ModelInternalInitializer.cpp [73/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/meson-generated_.._UnanimityVersion.cpp.o' -MF 'src/25a6634@@unanimity@sha/meson-generated_.._UnanimityVersion.cpp.o.d' -o 'src/25a6634@@unanimity@sha/meson-generated_.._UnanimityVersion.cpp.o' -c src/UnanimityVersion.cpp [74/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/.._third-party_cssw_ssw_cpp.cpp.o' -MF 'src/25a6634@@unanimity@sha/.._third-party_cssw_ssw_cpp.cpp.o.d' -o 'src/25a6634@@unanimity@sha/.._third-party_cssw_ssw_cpp.cpp.o' -c ../third-party/cssw/ssw_cpp.cpp FAILED: src/25a6634@@unanimity@sha/.._third-party_cssw_ssw_cpp.cpp.o /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity@sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity@sha/.._third-party_cssw_ssw_cpp.cpp.o' -MF 'src/25a6634@@unanimity@sha/.._third-party_cssw_ssw_cpp.cpp.o.d' -o 'src/25a6634@@unanimity@sha/.._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 /nxb-bin/usr/lib/clang/6.0.1/include/emmintrin.h:27: In file included from /nxb-bin/usr/lib/clang/6.0.1/include/xmmintrin.h:27: /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:47:5: error: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'? __builtin_ia32_emms(); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:47:5: note: '__builtin_isless' declared here /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:47:25: error: too few arguments to function call, expected 2, have 0 __builtin_ia32_emms(); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:64:19: error: use of undeclared identifier '__builtin_ia32_vec_init_v2si' return (__m64)__builtin_ia32_vec_init_v2si(__i, 0); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:81:12: error: use of undeclared identifier '__builtin_ia32_vec_ext_v2si' return __builtin_ia32_vec_ext_v2si((__v2si)__m, 0); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:143:19: error: use of undeclared identifier '__builtin_ia32_packsswb' return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:173:19: error: use of undeclared identifier '__builtin_ia32_packssdw' return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:203:19: error: use of undeclared identifier '__builtin_ia32_packuswb' return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:230:19: error: use of undeclared identifier '__builtin_ia32_punpckhbw' return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:253:19: error: use of undeclared identifier '__builtin_ia32_punpckhwd' return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:274:19: error: use of undeclared identifier '__builtin_ia32_punpckhdq' return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:301:19: error: use of undeclared identifier '__builtin_ia32_punpcklbw' return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:324:19: error: use of undeclared identifier '__builtin_ia32_punpcklwd' return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:345:19: error: use of undeclared identifier '__builtin_ia32_punpckldq' return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:366:19: error: use of undeclared identifier '__builtin_ia32_paddb' return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:387:19: error: use of undeclared identifier '__builtin_ia32_paddw' return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:408:19: error: use of undeclared identifier '__builtin_ia32_paddd' return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:430:19: error: use of undeclared identifier '__builtin_ia32_paddsb' return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:453:19: error: use of undeclared identifier '__builtin_ia32_paddsw' return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2); ^ /nxb-bin/usr/lib/clang/6.0.1/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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