------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/spoa XDG_CONFIG_HOME=/construction/biology/spoa HOME=/construction/biology/spoa TMPDIR="/tmp" PATH=/construction/biology/spoa/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/spoa XDG_CONFIG_HOME=/construction/biology/spoa HOME=/construction/biology/spoa TMPDIR="/tmp" PATH=/construction/biology/spoa/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lz -lcpu_features -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/spoa/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- CMAKE_BUILD_TYPE="release" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/spoa" EXAMPLESDIR="share/examples/spoa" DATADIR="share/spoa" WWWDIR="www/spoa" ETCDIR="etc/spoa" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/spoa DOCSDIR=/usr/local/share/doc/spoa EXAMPLESDIR=/usr/local/share/examples/spoa WWWDIR=/usr/local/www/spoa ETCDIR=/usr/local/etc/spoa SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600101 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/bioparser-3.0.12.2.txz Installing /packages/All/biosoup-g20201216.txz Installing /packages/All/icu-69.1,1.txz Installing /packages/All/boost-libs-1.72.0_5.txz ===== Message from boost-libs-1.72.0_5: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. Installing /packages/All/cereal-1.3.0.10.txz Installing /packages/All/simde-0.7.2.txz Installing /packages/All/libnghttp2-1.43.0.txz Installing /packages/All/ca_root_nss-3.63.txz ===== Message from ca_root_nss-3.63: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/openssl-1.1.1k_1,1.txz Installing /packages/All/curl-7.77.0.txz Installing /packages/All/expat-2.4.1.txz Installing /packages/All/libuv-1.41.0.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/rhash-1.4.1.txz Installing /packages/All/liblz4-1.9.3,1.txz Installing /packages/All/libarchive-3.5.1,1.txz Installing /packages/All/ncurses-6.2.20210626.txz ===== Message from ncurses-6.2.20210626: -- { type: install message: < spoa-4.0.7_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> spoa-4.0.7_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by spoa-4.0.7_2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> spoa-4.0.7_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by spoa-4.0.7_2 for building => SHA256 Checksum OK for rvaser-spoa-4.0.7_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> spoa-4.0.7_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by spoa-4.0.7_2 for building ===> Extracting for spoa-4.0.7_2 => SHA256 Checksum OK for rvaser-spoa-4.0.7_GH0.tar.gz. Extracted Memory Use: 0.24M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for spoa-4.0.7_2 ===> Applying ports patches for spoa-4.0.7_2 from /xports/biology/spoa/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> spoa-4.0.7_2 depends on package: bioparser>0 - found ===> spoa-4.0.7_2 depends on file: /usr/local/include/biosoup/nucleic_acid.hpp - found ===> spoa-4.0.7_2 depends on package: cereal>0 - found ===> spoa-4.0.7_2 depends on package: simde>0 - found ===> spoa-4.0.7_2 depends on file: /usr/local/bin/cmake - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> spoa-4.0.7_2 depends on shared library: libcpu_features.so - found (/usr/local/lib/libcpu_features.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> spoa-4.0.7_2 depends on package: bioparser>0 - found ===> spoa-4.0.7_2 depends on file: /usr/local/include/biosoup/nucleic_acid.hpp - found ===> spoa-4.0.7_2 depends on package: cereal>0 - found ===> spoa-4.0.7_2 depends on package: simde>0 - found ===> spoa-4.0.7_2 depends on file: /usr/local/bin/cmake - found ===> spoa-4.0.7_2 depends on shared library: libcpu_features.so - found (/usr/local/lib/libcpu_features.so) ===> Configuring for spoa-4.0.7_2 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/spoa/.build -- The CXX compiler identification is GNU 8.3.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_COMPILER CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS THREADS_HAVE_PTHREAD_ARG spoa_optimize_for_native spoa_optimize_for_portability -- Build files have been written to: /construction/biology/spoa/.build SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for spoa-4.0.7_2 /usr/local/bin/cmake -S/construction/biology/spoa/spoa-4.0.7 -B/construction/biology/spoa/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/spoa/.build/CMakeFiles /construction/biology/spoa/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- CMakeFiles/spoa_avx2.dir/all --- --- CMakeFiles/spoa_sse4.1.dir/all --- --- CMakeFiles/spoa_sse2.dir/all --- --- CMakeFiles/spoa_avx2.dir/all --- /usr/bin/make -f CMakeFiles/spoa_avx2.dir/build.make CMakeFiles/spoa_avx2.dir/depend --- CMakeFiles/spoa_sse2.dir/all --- /usr/bin/make -f CMakeFiles/spoa_sse2.dir/build.make CMakeFiles/spoa_sse2.dir/depend --- CMakeFiles/spoa_sse4.1.dir/all --- /usr/bin/make -f CMakeFiles/spoa_sse4.1.dir/build.make CMakeFiles/spoa_sse4.1.dir/depend --- CMakeFiles/spoa_avx2.dir/all --- --- CMakeFiles/spoa_avx2.dir/depend --- cd /construction/biology/spoa/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/spoa/spoa-4.0.7 /construction/biology/spoa/spoa-4.0.7 /construction/biology/spoa/.build /construction/biology/spoa/.build /construction/biology/spoa/.build/CMakeFiles/spoa_avx2.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/spoa_avx2.dir/build.make CMakeFiles/spoa_avx2.dir/build --- CMakeFiles/spoa_sse4.1.dir/all --- --- CMakeFiles/spoa_sse4.1.dir/depend --- --- CMakeFiles/spoa_avx2.dir/all --- --- CMakeFiles/spoa_avx2.dir/src/simd_alignment_engine_dispatch.cpp.o --- [ 8%] Building CXX object CMakeFiles/spoa_avx2.dir/src/simd_alignment_engine_dispatch.cpp.o --- CMakeFiles/spoa_sse2.dir/all --- --- CMakeFiles/spoa_sse2.dir/depend --- --- CMakeFiles/spoa_avx2.dir/all --- /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -I/construction/biology/spoa/spoa-4.0.7/include -I/construction/biology/spoa/spoa-4.0.7/vendor/simde -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -mavx2 -std=c++11 -MD -MT CMakeFiles/spoa_avx2.dir/src/simd_alignment_engine_dispatch.cpp.o -MF CMakeFiles/spoa_avx2.dir/src/simd_alignment_engine_dispatch.cpp.o.d -o CMakeFiles/spoa_avx2.dir/src/simd_alignment_engine_dispatch.cpp.o -c /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp --- CMakeFiles/spoa_sse2.dir/all --- cd /construction/biology/spoa/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/spoa/spoa-4.0.7 /construction/biology/spoa/spoa-4.0.7 /construction/biology/spoa/.build /construction/biology/spoa/.build /construction/biology/spoa/.build/CMakeFiles/spoa_sse2.dir/DependInfo.cmake --- CMakeFiles/spoa_sse4.1.dir/all --- cd /construction/biology/spoa/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/spoa/spoa-4.0.7 /construction/biology/spoa/spoa-4.0.7 /construction/biology/spoa/.build /construction/biology/spoa/.build /construction/biology/spoa/.build/CMakeFiles/spoa_sse4.1.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/spoa_sse4.1.dir/build.make CMakeFiles/spoa_sse4.1.dir/build --- CMakeFiles/spoa_sse4.1.dir/src/simd_alignment_engine_dispatch.cpp.o --- [ 16%] Building CXX object CMakeFiles/spoa_sse4.1.dir/src/simd_alignment_engine_dispatch.cpp.o /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -I/construction/biology/spoa/spoa-4.0.7/include -I/construction/biology/spoa/spoa-4.0.7/vendor/simde -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -msse4.1 -std=c++11 -MD -MT CMakeFiles/spoa_sse4.1.dir/src/simd_alignment_engine_dispatch.cpp.o -MF CMakeFiles/spoa_sse4.1.dir/src/simd_alignment_engine_dispatch.cpp.o.d -o CMakeFiles/spoa_sse4.1.dir/src/simd_alignment_engine_dispatch.cpp.o -c /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp --- CMakeFiles/spoa_sse2.dir/all --- /usr/bin/make -f CMakeFiles/spoa_sse2.dir/build.make CMakeFiles/spoa_sse2.dir/build --- CMakeFiles/spoa_sse2.dir/src/simd_alignment_engine_dispatch.cpp.o --- [ 25%] Building CXX object CMakeFiles/spoa_sse2.dir/src/simd_alignment_engine_dispatch.cpp.o /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -I/construction/biology/spoa/spoa-4.0.7/include -I/construction/biology/spoa/spoa-4.0.7/vendor/simde -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -msse2 -std=c++11 -MD -MT CMakeFiles/spoa_sse2.dir/src/simd_alignment_engine_dispatch.cpp.o -MF CMakeFiles/spoa_sse2.dir/src/simd_alignment_engine_dispatch.cpp.o.d -o CMakeFiles/spoa_sse2.dir/src/simd_alignment_engine_dispatch.cpp.o -c /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp --- CMakeFiles/spoa_avx2.dir/all --- In file included from /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp:3: /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:315:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> sequence_profile_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:320:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> M_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:328:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> masks_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:332:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> penalties_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Realloc(uint64_t, uint64_t, uint8_t)': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:432:65: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes] pimpl_->sequence_profile_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:446:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes] pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:462:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes] pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:480:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes] pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:491:54: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes] pimpl_->masks_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:501:58: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes] pimpl_->penalties_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In instantiation of 'T* spoa::AllocateAlignedMemory(T**, std::size_t, std::size_t) [with spoa::Architecture A = (spoa::Architecture)0; T = __vector(8) int; std::size_t = long unsigned int]': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:427:56: required from 'void spoa::SimdAlignmentEngine::Realloc(uint64_t, uint64_t, uint8_t) [with spoa::Architecture A = (spoa::Architecture)0; uint64_t = long unsigned int; uint8_t = unsigned char]' /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp:15:16: required from here /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:54:14: warning: 'new' of type '__vector(8) int' with extended alignment 32 [-Waligned-new=] *storage = new T[size + alignment - 1]; ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:54:14: note: uses 'void* operator new [](std::size_t)', which does not have an alignment parameter /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:54:14: note: use '-faligned-new' to enable C++17 over-aligned new support --- CMakeFiles/spoa_sse2.dir/all --- In file included from /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp:3: /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:315:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> sequence_profile_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:320:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> M_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:328:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> masks_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:332:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> penalties_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Realloc(uint64_t, uint64_t, uint8_t)': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:432:65: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->sequence_profile_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:446:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:462:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:480:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:491:54: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->masks_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:501:58: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->penalties_storage = std::unique_ptr<__mxxxi[]>(storage); ^ --- CMakeFiles/spoa_avx2.dir/all --- /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet<(spoa::Architecture)0, int>; spoa::Architecture A = (spoa::Architecture)0]': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] for (std::uint32_t i = 1; i < matrix_height; ++i) { ^~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:566:5: note: here case AlignmentSubtype::kAffine: ^~~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet<(spoa::Architecture)0, short int>; spoa::Architecture A = (spoa::Architecture)0]': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] for (std::uint32_t i = 1; i < matrix_height; ++i) { ^~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:566:5: note: here case AlignmentSubtype::kAffine: ^~~~ --- CMakeFiles/spoa_sse4.1.dir/all --- In file included from /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp:3: /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:315:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> sequence_profile_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:320:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> M_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:328:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> masks_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:332:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> penalties_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Realloc(uint64_t, uint64_t, uint8_t)': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:432:65: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->sequence_profile_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:446:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:462:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:480:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:491:54: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->masks_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:501:58: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->penalties_storage = std::unique_ptr<__mxxxi[]>(storage); ^ --- CMakeFiles/spoa_sse2.dir/all --- /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet<(spoa::Architecture)2, int>; spoa::Architecture A = (spoa::Architecture)2]': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] for (std::uint32_t i = 1; i < matrix_height; ++i) { ^~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:566:5: note: here case AlignmentSubtype::kAffine: ^~~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet<(spoa::Architecture)2, short int>; spoa::Architecture A = (spoa::Architecture)2]': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] for (std::uint32_t i = 1; i < matrix_height; ++i) { ^~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:566:5: note: here case AlignmentSubtype::kAffine: ^~~~ --- CMakeFiles/spoa_sse4.1.dir/all --- /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet<(spoa::Architecture)1, int>; spoa::Architecture A = (spoa::Architecture)1]': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] for (std::uint32_t i = 1; i < matrix_height; ++i) { ^~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:566:5: note: here case AlignmentSubtype::kAffine: ^~~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet<(spoa::Architecture)1, short int>; spoa::Architecture A = (spoa::Architecture)1]': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] for (std::uint32_t i = 1; i < matrix_height; ++i) { ^~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:566:5: note: here case AlignmentSubtype::kAffine: ^~~~ --- CMakeFiles/spoa_sse2.dir/all --- [ 25%] Built target spoa_sse2 --- CMakeFiles/spoa_avx2.dir/all --- [ 25%] Built target spoa_avx2 --- CMakeFiles/spoa_sse4.1.dir/all --- [ 25%] Built target spoa_sse4.1 --- CMakeFiles/spoa.dir/all --- /usr/bin/make -f CMakeFiles/spoa.dir/build.make CMakeFiles/spoa.dir/depend --- CMakeFiles/spoa.dir/depend --- cd /construction/biology/spoa/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/spoa/spoa-4.0.7 /construction/biology/spoa/spoa-4.0.7 /construction/biology/spoa/.build /construction/biology/spoa/.build /construction/biology/spoa/.build/CMakeFiles/spoa.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/spoa.dir/build.make CMakeFiles/spoa.dir/build --- CMakeFiles/spoa.dir/src/alignment_engine.cpp.o --- --- CMakeFiles/spoa.dir/src/graph.cpp.o --- --- CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o --- --- CMakeFiles/spoa.dir/src/dispatcher.cpp.o --- --- CMakeFiles/spoa.dir/src/graph.cpp.o --- [ 33%] Building CXX object CMakeFiles/spoa.dir/src/graph.cpp.o --- CMakeFiles/spoa.dir/src/dispatcher.cpp.o --- [ 41%] Building CXX object CMakeFiles/spoa.dir/src/dispatcher.cpp.o /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -Dspoa_EXPORTS -I/construction/biology/spoa/spoa-4.0.7/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -std=c++11 -MD -MT CMakeFiles/spoa.dir/src/dispatcher.cpp.o -MF CMakeFiles/spoa.dir/src/dispatcher.cpp.o.d -o CMakeFiles/spoa.dir/src/dispatcher.cpp.o -c /construction/biology/spoa/spoa-4.0.7/src/dispatcher.cpp --- CMakeFiles/spoa.dir/src/graph.cpp.o --- /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -Dspoa_EXPORTS -I/construction/biology/spoa/spoa-4.0.7/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -std=c++11 -MD -MT CMakeFiles/spoa.dir/src/graph.cpp.o -MF CMakeFiles/spoa.dir/src/graph.cpp.o.d -o CMakeFiles/spoa.dir/src/graph.cpp.o -c /construction/biology/spoa/spoa-4.0.7/src/graph.cpp --- CMakeFiles/spoa.dir/src/alignment_engine.cpp.o --- [ 50%] Building CXX object CMakeFiles/spoa.dir/src/alignment_engine.cpp.o /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -Dspoa_EXPORTS -I/construction/biology/spoa/spoa-4.0.7/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -std=c++11 -MD -MT CMakeFiles/spoa.dir/src/alignment_engine.cpp.o -MF CMakeFiles/spoa.dir/src/alignment_engine.cpp.o.d -o CMakeFiles/spoa.dir/src/alignment_engine.cpp.o -c /construction/biology/spoa/spoa-4.0.7/src/alignment_engine.cpp --- CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o --- [ 58%] Building CXX object CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -Dspoa_EXPORTS -I/construction/biology/spoa/spoa-4.0.7/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -std=c++11 -MD -MT CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o -MF CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o.d -o CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o -c /construction/biology/spoa/spoa-4.0.7/src/sisd_alignment_engine.cpp --- CMakeFiles/spoa.dir/src/dispatcher.cpp.o --- In file included from /construction/biology/spoa/spoa-4.0.7/src/dispatcher.cpp:3: /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:315:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> sequence_profile_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:320:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> M_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:328:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> masks_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:332:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] std::unique_ptr<__mxxxi[]> penalties_storage; ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Realloc(uint64_t, uint64_t, uint8_t)': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:432:65: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->sequence_profile_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:446:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:462:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:480:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:491:54: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->masks_storage = std::unique_ptr<__mxxxi[]>(storage); ^ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:501:58: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(2) long int []'} [-Wignored-attributes] pimpl_->penalties_storage = std::unique_ptr<__mxxxi[]>(storage); ^ --- CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o --- /construction/biology/spoa/spoa-4.0.7/src/sisd_alignment_engine.cpp: In member function 'void spoa::SisdAlignmentEngine::Initialize(const char*, uint32_t, const spoa::Graph&)': /construction/biology/spoa/spoa-4.0.7/src/sisd_alignment_engine.cpp:156:7: warning: this statement may fall through [-Wimplicit-fallthrough=] } ^ /construction/biology/spoa/spoa-4.0.7/src/sisd_alignment_engine.cpp:157:5: note: here case AlignmentSubtype::kAffine: ^~~~ /construction/biology/spoa/spoa-4.0.7/src/sisd_alignment_engine.cpp:173:7: warning: this statement may fall through [-Wimplicit-fallthrough=] } ^ /construction/biology/spoa/spoa-4.0.7/src/sisd_alignment_engine.cpp:174:5: note: here case AlignmentSubtype::kLinear: ^~~~ --- CMakeFiles/spoa.dir/src/dispatcher.cpp.o --- /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet<(spoa::Architecture)0, int>; spoa::Architecture A = (spoa::Architecture)0]': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] for (std::uint32_t i = 1; i < matrix_height; ++i) { ^~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:566:5: note: here case AlignmentSubtype::kAffine: ^~~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet<(spoa::Architecture)0, short int>; spoa::Architecture A = (spoa::Architecture)0]': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] for (std::uint32_t i = 1; i < matrix_height; ++i) { ^~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:566:5: note: here case AlignmentSubtype::kAffine: ^~~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet<(spoa::Architecture)1, int>; spoa::Architecture A = (spoa::Architecture)1]': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] for (std::uint32_t i = 1; i < matrix_height; ++i) { ^~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:566:5: note: here case AlignmentSubtype::kAffine: ^~~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet<(spoa::Architecture)1, short int>; spoa::Architecture A = (spoa::Architecture)1]': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] for (std::uint32_t i = 1; i < matrix_height; ++i) { ^~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:566:5: note: here case AlignmentSubtype::kAffine: ^~~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet<(spoa::Architecture)2, int>; spoa::Architecture A = (spoa::Architecture)2]': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] for (std::uint32_t i = 1; i < matrix_height; ++i) { ^~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:566:5: note: here case AlignmentSubtype::kAffine: ^~~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet<(spoa::Architecture)2, short int>; spoa::Architecture A = (spoa::Architecture)2]': /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] for (std::uint32_t i = 1; i < matrix_height; ++i) { ^~~ /construction/biology/spoa/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:566:5: note: here case AlignmentSubtype::kAffine: ^~~~ --- lib/libspoa.so.7.0.0 --- [ 66%] Linking CXX shared library lib/libspoa.so /usr/local/bin/cmake -E cmake_link_script CMakeFiles/spoa.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -lz -lcpu_features -L/usr/local/lib -shared -Wl,-soname,libspoa.so.7.0.0 -o lib/libspoa.so.7.0.0 CMakeFiles/spoa.dir/src/alignment_engine.cpp.o CMakeFiles/spoa.dir/src/graph.cpp.o CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o CMakeFiles/spoa.dir/src/dispatcher.cpp.o /usr/local/bin/cmake -E cmake_symlink_library lib/libspoa.so.7.0.0 lib/libspoa.so.7.0.0 lib/libspoa.so [ 75%] Built target spoa --- CMakeFiles/spoa_exe.dir/all --- /usr/bin/make -f CMakeFiles/spoa_exe.dir/build.make CMakeFiles/spoa_exe.dir/depend --- CMakeFiles/spoa_exe.dir/depend --- cd /construction/biology/spoa/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/spoa/spoa-4.0.7 /construction/biology/spoa/spoa-4.0.7 /construction/biology/spoa/.build /construction/biology/spoa/.build /construction/biology/spoa/.build/CMakeFiles/spoa_exe.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/spoa_exe.dir/build.make CMakeFiles/spoa_exe.dir/build --- CMakeFiles/spoa_exe.dir/src/main.cpp.o --- [ 83%] Building CXX object CMakeFiles/spoa_exe.dir/src/main.cpp.o /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DSPOA_VERSION=\"v4.0.7\" -DUSE_SIMDE -I/construction/biology/spoa/spoa-4.0.7/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -MD -MT CMakeFiles/spoa_exe.dir/src/main.cpp.o -MF CMakeFiles/spoa_exe.dir/src/main.cpp.o.d -o CMakeFiles/spoa_exe.dir/src/main.cpp.o -c /construction/biology/spoa/spoa-4.0.7/src/main.cpp --- bin/spoa --- [ 91%] Linking CXX executable bin/spoa /usr/local/bin/cmake -E cmake_link_script CMakeFiles/spoa_exe.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -lz -lcpu_features -L/usr/local/lib CMakeFiles/spoa_exe.dir/src/main.cpp.o -o bin/spoa -Wl,-z,origin,-rpath,/construction/biology/spoa/.build/lib lib/libspoa.so.7.0.0 [100%] Built target spoa_exe /usr/local/bin/cmake -E cmake_progress_start /construction/biology/spoa/.build/CMakeFiles 0 SUCCEEDED 00:01:07 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> spoa-4.0.7_2 depends on package: cereal>0 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for spoa-4.0.7_2 ===> spoa-4.0.7_2 depends on package: cereal>0 - found ===> Generating temporary packing list /usr/local/bin/cmake -S/construction/biology/spoa/spoa-4.0.7 -B/construction/biology/spoa/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/spoa/.build/CMakeFiles /construction/biology/spoa/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f CMakeFiles/spoa_avx2.dir/build.make CMakeFiles/spoa_avx2.dir/depend cd /construction/biology/spoa/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" 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CMakeFiles/CMakeRelink.dir/libspoa.so.7.0.0 CMakeFiles/spoa.dir/src/alignment_engine.cpp.o CMakeFiles/spoa.dir/src/graph.cpp.o CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o CMakeFiles/spoa.dir/src/dispatcher.cpp.o /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libspoa.so.7.0.0 CMakeFiles/CMakeRelink.dir/libspoa.so.7.0.0 CMakeFiles/CMakeRelink.dir/libspoa.so Installing the project stripped... /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /construction/biology/spoa/stage/usr/local/lib/libspoa.so.7.0.0 -- Installing: /construction/biology/spoa/stage/usr/local/lib/libspoa.so -- Installing: /construction/biology/spoa/stage/usr/local/include/spoa -- Installing: /construction/biology/spoa/stage/usr/local/include/spoa/alignment_engine.hpp -- Installing: /construction/biology/spoa/stage/usr/local/include/spoa/architectures.hpp -- Installing: /construction/biology/spoa/stage/usr/local/include/spoa/graph.hpp -- Installing: /construction/biology/spoa/stage/usr/local/include/spoa/spoa.hpp -- Installing: /construction/biology/spoa/stage/usr/local/lib/pkgconfig/spoa-1.pc -- Installing: /construction/biology/spoa/stage/usr/local/bin/spoa ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 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