------------------------------------------------------------------------------- -- 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/diamond XDG_CONFIG_HOME=/construction/biology/diamond HOME=/construction/biology/diamond TMPDIR="/tmp" PATH=/construction/biology/diamond/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/diamond XDG_CONFIG_HOME=/construction/biology/diamond HOME=/construction/biology/diamond TMPDIR="/tmp" PATH=/construction/biology/diamond/.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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/diamond/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/diamond" EXAMPLESDIR="share/examples/diamond" DATADIR="share/diamond" WWWDIR="www/diamond" ETCDIR="etc/diamond" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/diamond DOCSDIR=/usr/local/share/doc/diamond EXAMPLESDIR=/usr/local/share/examples/diamond WWWDIR=/usr/local/www/diamond ETCDIR=/usr/local/etc/diamond 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/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: < diamond-2.0.9 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> diamond-2.0.9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by diamond-2.0.9 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> diamond-2.0.9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by diamond-2.0.9 for building => SHA256 Checksum OK for bbuchfink-diamond-v2.0.9_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> diamond-2.0.9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by diamond-2.0.9 for building ===> Extracting for diamond-2.0.9 => SHA256 Checksum OK for bbuchfink-diamond-v2.0.9_GH0.tar.gz. Extracted Memory Use: 8.80M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for diamond-2.0.9 ===> Applying dragonfly patches for diamond-2.0.9 from /xports/biology/diamond/dragonfly SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> diamond-2.0.9 depends on file: /usr/local/bin/cmake - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> diamond-2.0.9 depends on file: /usr/local/bin/cmake - found ===> Configuring for diamond-2.0.9 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/diamond/.build CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAS_GNUPP14 -- Performing Test HAS_GNUPP14 - Success -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") -- Looking for pthread.h -- Looking for pthread.h - found -- Found Threads: TRUE -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS -- Build files have been written to: /construction/biology/diamond/.build SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for diamond-2.0.9 /usr/local/bin/cmake -S/construction/biology/diamond/diamond-2.0.9 -B/construction/biology/diamond/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/diamond/.build/CMakeFiles /construction/biology/diamond/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- CMakeFiles/arch_sse4_1.dir/all --- --- CMakeFiles/arch_generic.dir/all --- --- CMakeFiles/arch_avx2.dir/all --- --- CMakeFiles/arch_sse4_1.dir/all --- /usr/bin/make -f CMakeFiles/arch_sse4_1.dir/build.make CMakeFiles/arch_sse4_1.dir/depend --- CMakeFiles/arch_generic.dir/all --- /usr/bin/make -f CMakeFiles/arch_generic.dir/build.make CMakeFiles/arch_generic.dir/depend --- CMakeFiles/arch_avx2.dir/all --- /usr/bin/make -f CMakeFiles/arch_avx2.dir/build.make CMakeFiles/arch_avx2.dir/depend --- CMakeFiles/arch_sse4_1.dir/all --- --- CMakeFiles/arch_sse4_1.dir/depend --- --- CMakeFiles/arch_generic.dir/all --- --- CMakeFiles/arch_generic.dir/depend --- --- CMakeFiles/arch_sse4_1.dir/all --- cd /construction/biology/diamond/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/diamond/diamond-2.0.9 /construction/biology/diamond/diamond-2.0.9 /construction/biology/diamond/.build /construction/biology/diamond/.build /construction/biology/diamond/.build/CMakeFiles/arch_sse4_1.dir/DependInfo.cmake --- CMakeFiles/arch_generic.dir/all --- cd /construction/biology/diamond/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/diamond/diamond-2.0.9 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CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe.cpp.o --- --- CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_swipe.cpp.o --- --- CMakeFiles/arch_sse4_1.dir/src/search/stage2.cpp.o --- --- CMakeFiles/arch_sse4_1.dir/src/tools/benchmark.cpp.o --- --- CMakeFiles/arch_generic.dir/all --- --- CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- --- CMakeFiles/arch_generic.dir/src/dp/swipe/swipe.cpp.o --- --- CMakeFiles/arch_generic.dir/src/dp/swipe/banded_swipe.cpp.o --- --- CMakeFiles/arch_generic.dir/src/search/stage2.cpp.o --- --- CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- [ 3%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- CMakeFiles/arch_generic.dir/src/dp/swipe/swipe.cpp.o --- [ 3%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/swipe.cpp.o --- CMakeFiles/arch_sse4_1.dir/all --- [ 3%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/tools/benchmark.cpp.o --- CMakeFiles/arch_generic.dir/all --- --- CMakeFiles/arch_generic.dir/src/dp/swipe/banded_swipe.cpp.o --- [ 3%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/banded_swipe.cpp.o --- CMakeFiles/arch_sse4_1.dir/all --- --- CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- [ 3%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- CMakeFiles/arch_generic.dir/all --- --- CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.9/src/lib -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -std=gnu++14 -MD -MT 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-DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.9/src/lib -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -std=gnu++14 -MD -MT CMakeFiles/arch_generic.dir/src/dp/swipe/swipe.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/swipe/swipe.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/swipe/swipe.cpp.o -c /construction/biology/diamond/diamond-2.0.9/src/dp/swipe/swipe.cpp --- CMakeFiles/arch_avx2.dir/all --- /usr/bin/make -f CMakeFiles/arch_avx2.dir/build.make CMakeFiles/arch_avx2.dir/build --- CMakeFiles/arch_sse4_1.dir/all --- --- CMakeFiles/arch_sse4_1.dir/src/search/stage2.cpp.o --- [ 3%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/search/stage2.cpp.o --- 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