=>> Building biology/diamond build started at Thu Mar 12 03:31:47 EDT 2026 port directory: /usr/ports/biology/diamond package name: diamond-2.1.23 building for: FreeBSD pkg.DaveG.ca 14.4-RELEASE FreeBSD 14.4-RELEASE 1404000 amd64 maintained by: jrm@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 451 Mar 6 20:23 /usr/ports/biology/diamond/Makefile Ports top last git commit: 26b198eb3ee3 Ports top unclean checkout: no Port dir last git commit: 9457a54a3f6d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1404000 Job Id: 07 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE 1404000 UNAME_r=14.4-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_4_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jrm@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/diamond/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/diamond/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/diamond/work/.cache HOME=/wrkdirs/usr/ports/biology/diamond/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/diamond/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/diamond/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/diamond/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/diamond/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/diamond/work/.cache HOME=/wrkdirs/usr/ports/biology/diamond/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/diamond/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/diamond/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/diamond/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" OSREL=14.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/diamond" EXAMPLESDIR="share/examples/diamond" DATADIR="share/diamond" WWWDIR="www/diamond" ETCDIR="etc/diamond" --End PLIST_SUB-- --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 --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.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) 8192 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 pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> diamond-2.1.23 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> diamond-2.1.23 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of diamond-2.1.23 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 => bbuchfink-diamond-v2.1.23_GH0.tar.gz doesn't seem to exist in /portdistfiles. => Attempting to fetch https://codeload.github.com/bbuchfink/diamond/tar.gz/v2.1.23?dummy=/bbuchfink-diamond-v2.1.23_GH0.tar.gz fetch: https://codeload.github.com/bbuchfink/diamond/tar.gz/v2.1.23?dummy=/bbuchfink-diamond-v2.1.23_GH0.tar.gz: size unknown fetch: https://codeload.github.com/bbuchfink/diamond/tar.gz/v2.1.23?dummy=/bbuchfink-diamond-v2.1.23_GH0.tar.gz: size of remote file is not known bbuchfink-diamond-v2.1.23_GH0.tar.gz 1106 kB 1211 kBps 01s ===> Fetching all distfiles required by diamond-2.1.23 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by diamond-2.1.23 for building => SHA256 Checksum OK for bbuchfink-diamond-v2.1.23_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by diamond-2.1.23 for building ===> Extracting for diamond-2.1.23 => SHA256 Checksum OK for bbuchfink-diamond-v2.1.23_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for diamond-2.1.23 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> diamond-2.1.23 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.10_1.pkg [pkg.DaveG.ca] Installing cmake-core-3.31.10_1... [pkg.DaveG.ca] `-- Installing expat-2.7.4... [pkg.DaveG.ca] `-- Extracting expat-2.7.4: .......... done [pkg.DaveG.ca] `-- Installing jsoncpp-1.9.6_1... [pkg.DaveG.ca] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg.DaveG.ca] `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Installing libunistring-1.4.2... [pkg.DaveG.ca] | `-- Extracting libunistring-1.4.2: .......... done [pkg.DaveG.ca] `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] `-- Installing libuv-1.52.0... [pkg.DaveG.ca] `-- Extracting libuv-1.52.0: .......... done [pkg.DaveG.ca] `-- Installing rhash-1.4.6... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] `-- Extracting rhash-1.4.6: .......... done [pkg.DaveG.ca] Extracting cmake-core-3.31.10_1: .......... done ===> diamond-2.1.23 depends on file: /usr/local/bin/cmake - found ===> Returning to build of diamond-2.1.23 ===> diamond-2.1.23 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.13.2,4.pkg [pkg.DaveG.ca] Installing ninja-1.13.2,4... [pkg.DaveG.ca] `-- Installing python311-3.11.15... [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.3... [pkg.DaveG.ca] | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.15: .......... done [pkg.DaveG.ca] Extracting ninja-1.13.2,4: ..... done ===== Message from python311-3.11.15: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> diamond-2.1.23 depends on executable: ninja - found ===> Returning to build of diamond-2.1.23 ===> diamond-2.1.23 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> diamond-2.1.23 depends on file: /usr/local/bin/ccache - found ===> Returning to build of diamond-2.1.23 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> diamond-2.1.23 depends on shared library: libsqlite3.so - not found ===> Installing existing package /packages/All/sqlite3-3.50.4_2,1.pkg [pkg.DaveG.ca] Installing sqlite3-3.50.4_2,1... [pkg.DaveG.ca] `-- Installing libedit-3.1.20251016_1,1... [pkg.DaveG.ca] `-- Extracting libedit-3.1.20251016_1,1: .......... done [pkg.DaveG.ca] Extracting sqlite3-3.50.4_2,1: .......... done ===> diamond-2.1.23 depends on shared library: libsqlite3.so - found (/usr/local/lib/libsqlite3.so) ===> Returning to build of diamond-2.1.23 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for diamond-2.1.23 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/diamond/work/.build CMake Deprecation Warning at CMakeLists.txt:16 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is Clang 19.1.7 -- The CXX compiler identification is Clang 19.1.7 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/libexec/ccache/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/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of ptrdiff_t -- Check size of ptrdiff_t - done -- Check size of int -- Check size of int - done -- Performing Test HAS_GNUPP14 -- Performing Test HAS_GNUPP14 - Success -- Performing Test HAS_GNUPP17 -- Performing Test HAS_GNUPP17 - Success -- Performing Test HAS_GNUPP20 -- Performing Test HAS_GNUPP20 - Success -- Performing Test HAS_GNUPP23 -- Performing Test HAS_GNUPP23 - Success -- Looking for sysinfo -- Looking for sysinfo - not found -- Found ZLIB: /usr/lib/libz.so (found version "1.3.1") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for getauxval -- Looking for getauxval - not found -- SQLite3 Library: /usr/local/lib/libsqlite3.so -- Configuring done (6.2s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /wrkdirs/usr/ports/biology/diamond/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for diamond-2.1.23 [ 0% 64/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/util/io/file_source.cpp.o -MF CMakeFiles/diamond.dir/src/util/io/file_source.cpp.o.d -o CMakeFiles/diamond.dir/src/util/io/file_source.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/io/file_source.cpp [ 1% 65/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough 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-I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/util/simd.cpp.o -MF CMakeFiles/diamond.dir/src/util/simd.cpp.o.d -o CMakeFiles/diamond.dir/src/util/simd.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/simd.cpp [ 2% 68/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 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included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/tools/benchmark.cpp:52: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hit_buffer.h:39: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/queue.h:24: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/../parallel/semaphore.h:24:2: warning: "Old compiler missing semaphore support." 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[ 27% 114/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/lib/alp/njn_random.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/njn_random.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/njn_random.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib/alp/njn_random.cpp [ 28% 115/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -MD -MT CMakeFiles/arch_avx2.dir/src/dp/swipe/anchored_wrapper.cpp.o -MF CMakeFiles/arch_avx2.dir/src/dp/swipe/anchored_wrapper.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/dp/swipe/anchored_wrapper.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/dp/swipe/anchored_wrapper.cpp [ 28% 116/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -MD -MT CMakeFiles/arch_avx2.dir/src/tools/benchmark.cpp.o -MF CMakeFiles/arch_avx2.dir/src/tools/benchmark.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/tools/benchmark.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/tools/benchmark.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/tools/benchmark.cpp:52: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hit_buffer.h:39: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/queue.h:24: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/../parallel/semaphore.h:24:2: warning: "Old compiler missing semaphore support." [-W#warnings] 24 | #warning "Old compiler missing semaphore support." | ^ 1 warning generated. [ 29% 117/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/output/target_culling.cpp.o -MF CMakeFiles/diamond.dir/src/output/target_culling.cpp.o.d -o 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[-W#warnings] 24 | #warning "Old compiler missing semaphore support." | ^ 1 warning generated. 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/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hamming/stage1_2.cpp:32: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hamming/../stage2.h:33: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hamming/../search.h:38: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hamming/../hit_buffer.h:39: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/queue.h:24: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/../parallel/semaphore.h:24:2: warning: "Old compiler missing semaphore support." [-W#warnings] 24 | #warning "Old compiler missing semaphore support." | ^ 1 warning generated. 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[-W#warnings] 24 | #warning "Old compiler missing semaphore support." | ^ 1 warning generated. [ 36% 130/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/lib/alp/njn_dynprogprobproto.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/njn_dynprogprobproto.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/njn_dynprogprobproto.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib/alp/njn_dynprogprobproto.cpp [ 36% 131/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/lib/blast/nlm_linear_algebra.cpp.o -MF CMakeFiles/diamond.dir/src/lib/blast/nlm_linear_algebra.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/blast/nlm_linear_algebra.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib/blast/nlm_linear_algebra.cpp [ 37% 132/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -MD -MT CMakeFiles/arch_avx2.dir/src/search/hamming/stage1_2.cpp.o -MF CMakeFiles/arch_avx2.dir/src/search/hamming/stage1_2.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/search/hamming/stage1_2.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hamming/stage1_2.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hamming/stage1_2.cpp:32: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hamming/../stage2.h:33: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hamming/../search.h:38: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hamming/../hit_buffer.h:39: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/queue.h:24: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/../parallel/semaphore.h:24:2: warning: "Old compiler missing semaphore support." 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[-W#warnings] 24 | #warning "Old compiler missing semaphore support." | ^ 1 warning generated. 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[ 84% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/util/tsv/file.cpp.o -MF CMakeFiles/diamond.dir/src/util/tsv/file.cpp.o.d -o CMakeFiles/diamond.dir/src/util/tsv/file.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/tsv/file.cpp [ 85% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/cluster/realign.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/realign.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/realign.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/realign.cpp [ 85% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/tools/tools.cpp.o -MF CMakeFiles/diamond.dir/src/tools/tools.cpp.o.d -o CMakeFiles/diamond.dir/src/tools/tools.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/tools/tools.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/tools/tools.cpp:42: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/search.h:38: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hit_buffer.h:39: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/queue.h:24: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/../parallel/semaphore.h:24:2: warning: "Old compiler missing semaphore support." [-W#warnings] 24 | #warning "Old compiler missing semaphore support." | ^ 1 warning generated. [ 86% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/data/blastdb/psq.cpp.o -MF CMakeFiles/diamond.dir/src/data/blastdb/psq.cpp.o.d -o CMakeFiles/diamond.dir/src/data/blastdb/psq.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/data/blastdb/psq.cpp [ 86% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o -MF CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o.d -o CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hit_buffer.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hit_buffer.cpp:35: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hit_buffer.h:39: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/queue.h:24: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/../parallel/semaphore.h:24:2: warning: "Old compiler missing semaphore support." [-W#warnings] 24 | #warning "Old compiler missing semaphore support." | ^ 1 warning generated. [ 87% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/data/blastdb/phr.cpp.o -MF CMakeFiles/diamond.dir/src/data/blastdb/phr.cpp.o.d -o 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CMakeFiles/diamond.dir/src/output/daa/merge.cpp.o -MF CMakeFiles/diamond.dir/src/output/daa/merge.cpp.o.d -o CMakeFiles/diamond.dir/src/output/daa/merge.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/output/daa/merge.cpp [ 88% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/data/blastdb/pal.cpp.o -MF CMakeFiles/diamond.dir/src/data/blastdb/pal.cpp.o.d -o CMakeFiles/diamond.dir/src/data/blastdb/pal.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/data/blastdb/pal.cpp [ 89% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/util/tsv/table.cpp.o -MF CMakeFiles/diamond.dir/src/util/tsv/table.cpp.o.d -o CMakeFiles/diamond.dir/src/util/tsv/table.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/tsv/table.cpp [ 89% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/data/blastdb/pin.cpp.o -MF CMakeFiles/diamond.dir/src/data/blastdb/pin.cpp.o.d -o CMakeFiles/diamond.dir/src/data/blastdb/pin.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/data/blastdb/pin.cpp [ 90% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/data/block/block.cpp.o -MF CMakeFiles/diamond.dir/src/data/block/block.cpp.o.d -o CMakeFiles/diamond.dir/src/data/block/block.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/data/block/block.cpp [ 90% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/cluster/external/align.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/external/align.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/external/align.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/align.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/align.cpp:25: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:88:12: warning: taking address of packed member 'rep_oid' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 88 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:89:12: warning: taking address of packed member 'member_oid' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 89 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:90:12: warning: taking address of packed member 'rep_len' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 90 | in.read(&e.rep_len); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:91:12: warning: taking address of packed member 'member_len' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 91 | in.read(&e.member_len); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:121:12: warning: taking address of packed member 'rep_oid' of class or structure 'PairEntryShort' may result in an unaligned pointer value [-Waddress-of-packed-member] 121 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:122:12: warning: taking address of packed member 'member_oid' of class or structure 'PairEntryShort' may result in an unaligned pointer value [-Waddress-of-packed-member] 122 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:165:12: warning: taking address of packed member 'rep_oid' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:166:12: warning: taking address of packed member 'member_oid' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 166 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:167:12: warning: taking address of packed member 'rep_len' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | in.read(&e.rep_len); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:168:12: warning: taking address of packed member 'member_len' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 168 | in.read(&e.member_len); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:198:12: warning: taking address of packed member 'member_oid' of class or structure 'Assignment' may result in an unaligned pointer value [-Waddress-of-packed-member] 198 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:199:12: warning: taking address of packed member 'rep_oid' of class or structure 'Assignment' may result in an unaligned pointer value [-Waddress-of-packed-member] 199 | in.read(&e.rep_oid); | ^~~~~~~~~ 12 warnings generated. [ 91% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/cluster/external/output.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/external/output.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/external/output.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/output.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/output.cpp:25: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:88:12: warning: taking address of packed member 'rep_oid' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 88 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:89:12: warning: taking address of packed member 'member_oid' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 89 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:90:12: warning: taking address of packed member 'rep_len' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 90 | in.read(&e.rep_len); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:91:12: warning: taking address of packed member 'member_len' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 91 | in.read(&e.member_len); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:121:12: warning: taking address of packed member 'rep_oid' of class or structure 'PairEntryShort' may result in an unaligned pointer value [-Waddress-of-packed-member] 121 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:122:12: warning: taking address of packed member 'member_oid' of class or structure 'PairEntryShort' may result in an unaligned pointer value [-Waddress-of-packed-member] 122 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:165:12: warning: taking address of packed member 'rep_oid' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:166:12: warning: taking address of packed member 'member_oid' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 166 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:167:12: warning: taking address of packed member 'rep_len' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | in.read(&e.rep_len); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:168:12: warning: taking address of packed member 'member_len' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 168 | in.read(&e.member_len); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:198:12: warning: taking address of packed member 'member_oid' of class or structure 'Assignment' may result in an unaligned pointer value [-Waddress-of-packed-member] 198 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:199:12: warning: taking address of packed member 'rep_oid' of class or structure 'Assignment' may result in an unaligned pointer value [-Waddress-of-packed-member] 199 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/output.cpp:72:17: warning: comparison of integers of different signs: 'const value_type' (aka 'const unsigned long') and 'int64_t' (aka 'long') [-Wsign-compare] 72 | if (merged[i] == i) | ~~~~~~~~~ ^ ~ 13 warnings generated. [ 91% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/tools/greedy_vertex_cover.cpp.o -MF CMakeFiles/diamond.dir/src/tools/greedy_vertex_cover.cpp.o.d -o CMakeFiles/diamond.dir/src/tools/greedy_vertex_cover.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/tools/greedy_vertex_cover.cpp [ 92% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/cascaded/wrapper.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/cascaded/wrapper.cpp:26: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/search.h:38: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hit_buffer.h:39: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/queue.h:24: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/../parallel/semaphore.h:24:2: warning: "Old compiler missing semaphore support." [-W#warnings] 24 | #warning "Old compiler missing semaphore support." | ^ 1 warning generated. [ 92% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/cluster/external/seed_table.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/external/seed_table.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/external/seed_table.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/seed_table.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/seed_table.cpp:24: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/search.h:38: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hit_buffer.h:39: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/queue.h:24: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/../parallel/semaphore.h:24:2: warning: "Old compiler missing semaphore support." [-W#warnings] 24 | #warning "Old compiler missing semaphore support." | ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/seed_table.cpp:25: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:88:12: warning: taking address of packed member 'rep_oid' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 88 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:89:12: warning: taking address of packed member 'member_oid' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 89 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:90:12: warning: taking address of packed member 'rep_len' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 90 | in.read(&e.rep_len); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:91:12: warning: taking address of packed member 'member_len' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 91 | in.read(&e.member_len); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:121:12: warning: taking address of packed member 'rep_oid' of class or structure 'PairEntryShort' may result in an unaligned pointer value [-Waddress-of-packed-member] 121 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:122:12: warning: taking address of packed member 'member_oid' of class or structure 'PairEntryShort' may result in an unaligned pointer value [-Waddress-of-packed-member] 122 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:165:12: warning: taking address of packed member 'rep_oid' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:166:12: warning: taking address of packed member 'member_oid' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 166 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:167:12: warning: taking address of packed member 'rep_len' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | in.read(&e.rep_len); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:168:12: warning: taking address of packed member 'member_len' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 168 | in.read(&e.member_len); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:198:12: warning: taking address of packed member 'member_oid' of class or structure 'Assignment' may result in an unaligned pointer value [-Waddress-of-packed-member] 198 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:199:12: warning: taking address of packed member 'rep_oid' of class or structure 'Assignment' may result in an unaligned pointer value [-Waddress-of-packed-member] 199 | in.read(&e.rep_oid); | ^~~~~~~~~ 13 warnings generated. [ 93% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -MD -MT CMakeFiles/arch_generic.dir/src/dp/swipe/swipe_wrapper.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/swipe/swipe_wrapper.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/swipe/swipe_wrapper.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/dp/swipe/swipe_wrapper.cpp [ 94% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o -MF CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o.d -o CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/data/blastdb/blastdb.cpp [ 94% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/align/global_ranking/table.cpp.o -MF CMakeFiles/diamond.dir/src/align/global_ranking/table.cpp.o.d -o CMakeFiles/diamond.dir/src/align/global_ranking/table.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/align/global_ranking/table.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/align/global_ranking/table.cpp:29: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/search.h:38: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hit_buffer.h:39: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/queue.h:24: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/../parallel/semaphore.h:24:2: warning: "Old compiler missing semaphore support." [-W#warnings] 24 | #warning "Old compiler missing semaphore support." | ^ 1 warning generated. [ 95% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/data/dmnd/dmnd.cpp.o -MF CMakeFiles/diamond.dir/src/data/dmnd/dmnd.cpp.o.d -o CMakeFiles/diamond.dir/src/data/dmnd/dmnd.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/data/dmnd/dmnd.cpp [ 95% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/output/blast_tab_format.cpp.o -MF CMakeFiles/diamond.dir/src/output/blast_tab_format.cpp.o.d -o CMakeFiles/diamond.dir/src/output/blast_tab_format.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/output/blast_tab_format.cpp [ 96% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/cluster/external/pair_table.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/external/pair_table.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/external/pair_table.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/pair_table.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/pair_table.cpp:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/build_pair_table.h:21: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:88:12: warning: taking address of packed member 'rep_oid' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 88 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:89:12: warning: taking address of packed member 'member_oid' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 89 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:90:12: warning: taking address of packed member 'rep_len' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 90 | in.read(&e.rep_len); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:91:12: warning: taking address of packed member 'member_len' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 91 | in.read(&e.member_len); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:121:12: warning: taking address of packed member 'rep_oid' of class or structure 'PairEntryShort' may result in an unaligned pointer value [-Waddress-of-packed-member] 121 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:122:12: warning: taking address of packed member 'member_oid' of class or structure 'PairEntryShort' may result in an unaligned pointer value [-Waddress-of-packed-member] 122 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:165:12: warning: taking address of packed member 'rep_oid' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:166:12: warning: taking address of packed member 'member_oid' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 166 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:167:12: warning: taking address of packed member 'rep_len' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | in.read(&e.rep_len); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:168:12: warning: taking address of packed member 'member_len' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 168 | in.read(&e.member_len); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:198:12: warning: taking address of packed member 'member_oid' of class or structure 'Assignment' may result in an unaligned pointer value [-Waddress-of-packed-member] 198 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:199:12: warning: taking address of packed member 'rep_oid' of class or structure 'Assignment' may result in an unaligned pointer value [-Waddress-of-packed-member] 199 | in.read(&e.rep_oid); | ^~~~~~~~~ 12 warnings generated. [ 96% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/cluster/helpers.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/helpers.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/helpers.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/helpers.cpp [ 97% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/cluster/external/cluster.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/external/cluster.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/external/cluster.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/cluster.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/cluster.cpp:27: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:88:12: warning: taking address of packed member 'rep_oid' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 88 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:89:12: warning: taking address of packed member 'member_oid' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 89 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:90:12: warning: taking address of packed member 'rep_len' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 90 | in.read(&e.rep_len); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:91:12: warning: taking address of packed member 'member_len' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 91 | in.read(&e.member_len); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:121:12: warning: taking address of packed member 'rep_oid' of class or structure 'PairEntryShort' may result in an unaligned pointer value [-Waddress-of-packed-member] 121 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:122:12: warning: taking address of packed member 'member_oid' of class or structure 'PairEntryShort' may result in an unaligned pointer value [-Waddress-of-packed-member] 122 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:165:12: warning: taking address of packed member 'rep_oid' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:166:12: warning: taking address of packed member 'member_oid' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 166 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:167:12: warning: taking address of packed member 'rep_len' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | in.read(&e.rep_len); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:168:12: warning: taking address of packed member 'member_len' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 168 | in.read(&e.member_len); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:198:12: warning: taking address of packed member 'member_oid' of class or structure 'Assignment' may result in an unaligned pointer value [-Waddress-of-packed-member] 198 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:199:12: warning: taking address of packed member 'rep_oid' of class or structure 'Assignment' may result in an unaligned pointer value [-Waddress-of-packed-member] 199 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/cluster.cpp:55:18: warning: comparison of integers of different signs: 'value_type' (aka 'unsigned long') and 'int64_t' (aka 'long') [-Wsign-compare] 55 | while (rep[r] != r) | ~~~~~~ ^ ~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/cluster.cpp:57:10: warning: comparison of integers of different signs: 'int64_t' (aka 'long') and 'value_type' (aka 'unsigned long') [-Wsign-compare] 57 | if (r != rep[i]) | ~ ^ ~~~~~~ 14 warnings generated. [ 97% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/data/sequence_file.cpp.o -MF CMakeFiles/diamond.dir/src/data/sequence_file.cpp.o.d -o CMakeFiles/diamond.dir/src/data/sequence_file.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/data/sequence_file.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/data/sequence_file.cpp:36: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/queue.h:24: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/../parallel/semaphore.h:24:2: warning: "Old compiler missing semaphore support." [-W#warnings] 24 | #warning "Old compiler missing semaphore support." | ^ 1 warning generated. [ 98% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -MD -MT CMakeFiles/diamond.dir/src/cluster/external/external.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/external/external.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/external/external.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.cpp:34: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/search.h:38: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/search/hit_buffer.h:39: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/queue.h:24: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/util/data_structures/../parallel/semaphore.h:24:2: warning: "Old compiler missing semaphore support." [-W#warnings] 24 | #warning "Old compiler missing semaphore support." | ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.cpp:35: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:88:12: warning: taking address of packed member 'rep_oid' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 88 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:89:12: warning: taking address of packed member 'member_oid' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 89 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:90:12: warning: taking address of packed member 'rep_len' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 90 | in.read(&e.rep_len); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:91:12: warning: taking address of packed member 'member_len' of class or structure 'PairEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 91 | in.read(&e.member_len); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:121:12: warning: taking address of packed member 'rep_oid' of class or structure 'PairEntryShort' may result in an unaligned pointer value [-Waddress-of-packed-member] 121 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:122:12: warning: taking address of packed member 'member_oid' of class or structure 'PairEntryShort' may result in an unaligned pointer value [-Waddress-of-packed-member] 122 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:165:12: warning: taking address of packed member 'rep_oid' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:166:12: warning: taking address of packed member 'member_oid' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 166 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:167:12: warning: taking address of packed member 'rep_len' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | in.read(&e.rep_len); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:168:12: warning: taking address of packed member 'member_len' of class or structure 'Edge' may result in an unaligned pointer value [-Waddress-of-packed-member] 168 | in.read(&e.member_len); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:198:12: warning: taking address of packed member 'member_oid' of class or structure 'Assignment' may result in an unaligned pointer value [-Waddress-of-packed-member] 198 | in.read(&e.member_oid); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.h:199:12: warning: taking address of packed member 'rep_oid' of class or structure 'Assignment' may result in an unaligned pointer value [-Waddress-of-packed-member] 199 | in.read(&e.rep_oid); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.cpp:113:12: warning: taking address of packed member 'oid' of class or structure 'ChunkTableEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 113 | in.read(&e.oid); | ^~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/cluster/external/external.cpp:114:12: warning: taking address of packed member 'chunk' of class or structure 'ChunkTableEntry' may result in an unaligned pointer value [-Waddress-of-packed-member] 114 | in.read(&e.chunk); | ^~~~~~~ 15 warnings generated. [ 98% 183/184] /usr/local/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src -I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.23/src/lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++23 -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -MD -MT CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe_wrapper.cpp.o -MF CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe_wrapper.cpp.o.d -o 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/usr/local/lib/libsqlite3.so /usr/lib/libz.so -lpthread && : =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for diamond-2.1.23 ===> Generating temporary packing list [ 0% 1/1] cd /wrkdirs/usr/ports/biology/diamond/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/diamond/work/stage/usr/local/bin/diamond -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/diamond/work/stage/usr/local/bin/diamond" to "/usr/local/lib" ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-03-12T07:31:47+0000' 'PKG_NOTE_ports_top_git_hash=26b198eb3ee3' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=9457a54a3f6d' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for diamond-2.1.23 ===> Building diamond-2.1.23 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for diamond-2.1.23 build of biology/diamond | diamond-2.1.23 ended at Thu Mar 12 03:33:07 EDT 2026 build time: 00:01:21